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annotate qsub.err @ 13:ba7db5b70639 draft

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planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
author lecorguille
date Sun, 17 Apr 2016 16:36:55 -0400
parents db270f704d93
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
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2 SNIMissingWarning
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3 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
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4 InsecurePlatformWarning
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5 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
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6 SNIMissingWarning
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7 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
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8 InsecurePlatformWarning
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9 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
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10 You should consider upgrading via the 'pip install --upgrade pip' command.
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11 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
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12 You should consider upgrading via the 'pip install --upgrade pip' command.
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13 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
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14 SNIMissingWarning
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15 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
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16 InsecurePlatformWarning
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17 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
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18 You should consider upgrading via the 'pip install --upgrade pip' command.
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19 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
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20 SNIMissingWarning
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21 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
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22 InsecurePlatformWarning
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23 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
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24 You should consider upgrading via the 'pip install --upgrade pip' command.
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25 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
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26 You should consider upgrading via the 'pip install --upgrade pip' command.
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27 DEBUG:galaxy.app:python path is: /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/scripts, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/lib, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/lib, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/test, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
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28 INFO:galaxy.config:Logging at '10' level to 'stdout'
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29 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
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30 'storage.' % (dialect.name, dialect.driver))
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31 CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... FAIL
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32
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33 ======================================================================
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34 FAIL: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1
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35 ----------------------------------------------------------------------
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36 Traceback (most recent call last):
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37 File "/tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/test/functional/test_toolbox.py", line 299, in test_tool
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38 self.do_it( td )
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39 File "/tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/test/functional/test_toolbox.py", line 75, in do_it
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40 raise e
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41 JobOutputsError: Job in error state.
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42 Job in error state.
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43 Job in error state.
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44 -------------------- >> begin captured stdout << ---------------------
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45 History with id 2891970512fa2d5a in error - summary of datasets in error below.
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46 --------------------------------------
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47 | 3 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME)
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48 | Dataset Blurb:
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49 | error
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50 | Dataset Info:
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51 | PACKAGE INFO
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52 | parallel 3.1.2
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53 | BiocGenerics 0.14.0
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54 | Biobase 2.28.0
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55 | Rcpp 0.12.0
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56 | mzR 2.2.2
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57 | tcltk 3.1.2
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58 | igraph 0.7.1
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59 | xcms 1.44.0
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60 | snow 0.3.13
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61 | CAMERA 1.22.0
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62 | multtest 2.22.0
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63 | batch 1.1.4
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64 | ARGUMENTS INFO
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65 | xfunction annotatediff
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66 | image /tmp/714467.1.short.q/tmpR_swdX
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67 | Dataset Job Standard Output:
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68 | PACKAGE INFO
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69 | parallel 3.1.2
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70 | BiocGenerics 0.14.0
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71 | Biobase 2.28.0
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72 | Rcpp 0.12.0
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73 | mzR 2.2.2
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74 | tcltk 3.1.2
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75 | igraph 0.7.1
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76 | xcms 1.44.0
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77 | snow 0.3.13
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78 | CAMERA 1.22.0
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79 | multtest 2.22.0
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80 | batch 1.1.4
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81 | ARGUMENTS INFO
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82 | xfunction annotatediff
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83 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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84 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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85 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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86 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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87 | convert_param FALSE
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88 | num_digits 0
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89 | nSlaves 1
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90 | sigma 6
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91 | perfwhm 0.6
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92 | maxcharge 3
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93 | maxiso 4
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94 | minfrac 0.5
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95 | ppm 5
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96 | mzabs 0.015
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97 | intval into
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98 | max_peaks 100
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99 | quick FALSE
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100 | polarity negative
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101 | cor_eic_th 0.75
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102 | graphMethod hcs
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103 | pval 0.05
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104 | calcCiS TRUE
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105 | calcIso FALSE
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106 | calcCaS FALSE
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107 | multiplier 3
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108 | runDiffreport TRUE
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109 | eicmax 200
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110 | eicwidth 200
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111 | value into
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112 | sortpval FALSE
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113 | h 480
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114 | w 640
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115 | mzdec 2
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116 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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117 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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118 | INFILE PROCESSING INFO
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119 | ARGUMENTS PROCESSING INFO
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120 | MAIN PROCESSING INFO
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121 | Start grouping after retention time.
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122 | Created 1566 pseudospectra.
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123 | Generating peak matrix!
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124 | Run isotope peak annotation
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125 | % finished: 10 20 30 40 50 60 70 80 90 100
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126 | Found isotopes: 243
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127 | Start grouping after correlation.
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128 | Generating EIC's ..
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129 | Dataset Job Standard Error:
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130 | Fatal error: Exit code 1 ()
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131 | Error in getAllPeakEICs(object, index = index) :
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132 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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133 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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134 | Execution halted
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135 |
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136 --------------------------------------
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137 | 4 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME)
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138 | Dataset Blurb:
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139 | error
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140 | Dataset Info:
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141 | PACKAGE INFO
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142 | parallel 3.1.2
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143 | BiocGenerics 0.14.0
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144 | Biobase 2.28.0
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145 | Rcpp 0.12.0
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146 | mzR 2.2.2
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147 | tcltk 3.1.2
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148 | igraph 0.7.1
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149 | xcms 1.44.0
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150 | snow 0.3.13
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151 | CAMERA 1.22.0
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152 | multtest 2.22.0
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153 | batch 1.1.4
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154 | ARGUMENTS INFO
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155 | xfunction annotatediff
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156 | image /tmp/714467.1.short.q/tmpR_swdX
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157 | Dataset Job Standard Output:
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158 | PACKAGE INFO
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159 | parallel 3.1.2
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160 | BiocGenerics 0.14.0
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161 | Biobase 2.28.0
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162 | Rcpp 0.12.0
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163 | mzR 2.2.2
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164 | tcltk 3.1.2
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165 | igraph 0.7.1
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166 | xcms 1.44.0
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167 | snow 0.3.13
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168 | CAMERA 1.22.0
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169 | multtest 2.22.0
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170 | batch 1.1.4
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171 | ARGUMENTS INFO
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172 | xfunction annotatediff
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173 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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174 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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175 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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176 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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177 | convert_param FALSE
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178 | num_digits 0
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179 | nSlaves 1
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180 | sigma 6
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181 | perfwhm 0.6
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182 | maxcharge 3
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183 | maxiso 4
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184 | minfrac 0.5
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185 | ppm 5
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186 | mzabs 0.015
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187 | intval into
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188 | max_peaks 100
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189 | quick FALSE
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190 | polarity negative
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191 | cor_eic_th 0.75
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192 | graphMethod hcs
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193 | pval 0.05
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194 | calcCiS TRUE
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195 | calcIso FALSE
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196 | calcCaS FALSE
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197 | multiplier 3
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198 | runDiffreport TRUE
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199 | eicmax 200
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200 | eicwidth 200
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201 | value into
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202 | sortpval FALSE
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203 | h 480
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204 | w 640
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205 | mzdec 2
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206 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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207 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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208 | INFILE PROCESSING INFO
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209 | ARGUMENTS PROCESSING INFO
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210 | MAIN PROCESSING INFO
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211 | Start grouping after retention time.
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212 | Created 1566 pseudospectra.
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213 | Generating peak matrix!
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214 | Run isotope peak annotation
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215 | % finished: 10 20 30 40 50 60 70 80 90 100
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216 | Found isotopes: 243
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217 | Start grouping after correlation.
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218 | Generating EIC's ..
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219 | Dataset Job Standard Error:
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220 | Fatal error: Exit code 1 ()
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221 | Error in getAllPeakEICs(object, index = index) :
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222 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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223 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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224 | Execution halted
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225 |
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226 --------------------------------------
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227 | 5 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME)
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228 | Dataset Blurb:
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229 | error
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230 | Dataset Info:
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231 | PACKAGE INFO
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232 | parallel 3.1.2
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233 | BiocGenerics 0.14.0
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234 | Biobase 2.28.0
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235 | Rcpp 0.12.0
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236 | mzR 2.2.2
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237 | tcltk 3.1.2
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238 | igraph 0.7.1
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239 | xcms 1.44.0
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240 | snow 0.3.13
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241 | CAMERA 1.22.0
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242 | multtest 2.22.0
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243 | batch 1.1.4
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244 | ARGUMENTS INFO
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245 | xfunction annotatediff
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246 | image /tmp/714467.1.short.q/tmpR_swdX
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247 | Dataset Job Standard Output:
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248 | PACKAGE INFO
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249 | parallel 3.1.2
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250 | BiocGenerics 0.14.0
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251 | Biobase 2.28.0
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252 | Rcpp 0.12.0
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253 | mzR 2.2.2
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254 | tcltk 3.1.2
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255 | igraph 0.7.1
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256 | xcms 1.44.0
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257 | snow 0.3.13
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258 | CAMERA 1.22.0
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259 | multtest 2.22.0
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260 | batch 1.1.4
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261 | ARGUMENTS INFO
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262 | xfunction annotatediff
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263 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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264 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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265 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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266 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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267 | convert_param FALSE
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268 | num_digits 0
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269 | nSlaves 1
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270 | sigma 6
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271 | perfwhm 0.6
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272 | maxcharge 3
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273 | maxiso 4
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274 | minfrac 0.5
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275 | ppm 5
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276 | mzabs 0.015
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277 | intval into
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278 | max_peaks 100
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279 | quick FALSE
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280 | polarity negative
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281 | cor_eic_th 0.75
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282 | graphMethod hcs
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283 | pval 0.05
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284 | calcCiS TRUE
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285 | calcIso FALSE
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286 | calcCaS FALSE
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287 | multiplier 3
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288 | runDiffreport TRUE
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289 | eicmax 200
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290 | eicwidth 200
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291 | value into
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292 | sortpval FALSE
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293 | h 480
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294 | w 640
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295 | mzdec 2
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296 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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297 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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298 | INFILE PROCESSING INFO
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299 | ARGUMENTS PROCESSING INFO
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300 | MAIN PROCESSING INFO
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301 | Start grouping after retention time.
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302 | Created 1566 pseudospectra.
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303 | Generating peak matrix!
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304 | Run isotope peak annotation
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305 | % finished: 10 20 30 40 50 60 70 80 90 100
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306 | Found isotopes: 243
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307 | Start grouping after correlation.
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308 | Generating EIC's ..
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309 | Dataset Job Standard Error:
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310 | Fatal error: Exit code 1 ()
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311 | Error in getAllPeakEICs(object, index = index) :
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312 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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313 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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314 | Execution halted
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315 |
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316 --------------------------------------
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317 | 6 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME)
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318 | Dataset Blurb:
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319 | error
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320 | Dataset Info:
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321 | PACKAGE INFO
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322 | parallel 3.1.2
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323 | BiocGenerics 0.14.0
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324 | Biobase 2.28.0
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325 | Rcpp 0.12.0
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326 | mzR 2.2.2
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327 | tcltk 3.1.2
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328 | igraph 0.7.1
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329 | xcms 1.44.0
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330 | snow 0.3.13
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331 | CAMERA 1.22.0
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332 | multtest 2.22.0
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333 | batch 1.1.4
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334 | ARGUMENTS INFO
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335 | xfunction annotatediff
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336 | image /tmp/714467.1.short.q/tmpR_swdX
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337 | Dataset Job Standard Output:
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338 | PACKAGE INFO
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339 | parallel 3.1.2
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340 | BiocGenerics 0.14.0
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341 | Biobase 2.28.0
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342 | Rcpp 0.12.0
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343 | mzR 2.2.2
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344 | tcltk 3.1.2
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345 | igraph 0.7.1
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346 | xcms 1.44.0
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347 | snow 0.3.13
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348 | CAMERA 1.22.0
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349 | multtest 2.22.0
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350 | batch 1.1.4
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351 | ARGUMENTS INFO
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352 | xfunction annotatediff
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353 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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354 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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355 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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356 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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357 | convert_param FALSE
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358 | num_digits 0
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359 | nSlaves 1
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360 | sigma 6
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361 | perfwhm 0.6
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362 | maxcharge 3
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363 | maxiso 4
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364 | minfrac 0.5
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365 | ppm 5
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366 | mzabs 0.015
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367 | intval into
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368 | max_peaks 100
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369 | quick FALSE
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370 | polarity negative
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371 | cor_eic_th 0.75
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372 | graphMethod hcs
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373 | pval 0.05
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374 | calcCiS TRUE
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375 | calcIso FALSE
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376 | calcCaS FALSE
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377 | multiplier 3
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378 | runDiffreport TRUE
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379 | eicmax 200
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380 | eicwidth 200
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381 | value into
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382 | sortpval FALSE
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383 | h 480
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384 | w 640
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385 | mzdec 2
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386 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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387 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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388 | INFILE PROCESSING INFO
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389 | ARGUMENTS PROCESSING INFO
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390 | MAIN PROCESSING INFO
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391 | Start grouping after retention time.
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392 | Created 1566 pseudospectra.
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393 | Generating peak matrix!
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394 | Run isotope peak annotation
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395 | % finished: 10 20 30 40 50 60 70 80 90 100
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396 | Found isotopes: 243
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397 | Start grouping after correlation.
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398 | Generating EIC's ..
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399 | Dataset Job Standard Error:
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400 | Fatal error: Exit code 1 ()
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401 | Error in getAllPeakEICs(object, index = index) :
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402 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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403 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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404 | Execution halted
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405 |
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406 --------------------------------------
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407 History with id 2891970512fa2d5a in error - summary of datasets in error below.
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408 --------------------------------------
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409 | 3 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME)
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410 | Dataset Blurb:
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411 | error
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412 | Dataset Info:
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413 | PACKAGE INFO
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414 | parallel 3.1.2
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415 | BiocGenerics 0.14.0
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416 | Biobase 2.28.0
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417 | Rcpp 0.12.0
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418 | mzR 2.2.2
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419 | tcltk 3.1.2
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420 | igraph 0.7.1
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421 | xcms 1.44.0
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422 | snow 0.3.13
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423 | CAMERA 1.22.0
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424 | multtest 2.22.0
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425 | batch 1.1.4
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426 | ARGUMENTS INFO
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427 | xfunction annotatediff
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428 | image /tmp/714467.1.short.q/tmpR_swdX
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429 | Dataset Job Standard Output:
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430 | PACKAGE INFO
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431 | parallel 3.1.2
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432 | BiocGenerics 0.14.0
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433 | Biobase 2.28.0
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434 | Rcpp 0.12.0
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435 | mzR 2.2.2
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436 | tcltk 3.1.2
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437 | igraph 0.7.1
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438 | xcms 1.44.0
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439 | snow 0.3.13
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440 | CAMERA 1.22.0
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441 | multtest 2.22.0
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442 | batch 1.1.4
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443 | ARGUMENTS INFO
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444 | xfunction annotatediff
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445 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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446 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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447 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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448 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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449 | convert_param FALSE
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450 | num_digits 0
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451 | nSlaves 1
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452 | sigma 6
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453 | perfwhm 0.6
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454 | maxcharge 3
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455 | maxiso 4
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456 | minfrac 0.5
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457 | ppm 5
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458 | mzabs 0.015
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459 | intval into
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460 | max_peaks 100
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461 | quick FALSE
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462 | polarity negative
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463 | cor_eic_th 0.75
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464 | graphMethod hcs
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465 | pval 0.05
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466 | calcCiS TRUE
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467 | calcIso FALSE
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468 | calcCaS FALSE
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469 | multiplier 3
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470 | runDiffreport TRUE
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471 | eicmax 200
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472 | eicwidth 200
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473 | value into
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474 | sortpval FALSE
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475 | h 480
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476 | w 640
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477 | mzdec 2
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478 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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479 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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480 | INFILE PROCESSING INFO
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lecorguille
parents: 12
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481 | ARGUMENTS PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
482 | MAIN PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
483 | Start grouping after retention time.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
484 | Created 1566 pseudospectra.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
485 | Generating peak matrix!
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
486 | Run isotope peak annotation
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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487 | % finished: 10 20 30 40 50 60 70 80 90 100
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
488 | Found isotopes: 243
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
489 | Start grouping after correlation.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
490 | Generating EIC's ..
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diff changeset
491 | Dataset Job Standard Error:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
492 | Fatal error: Exit code 1 ()
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
493 | Error in getAllPeakEICs(object, index = index) :
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lecorguille
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diff changeset
494 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
495 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
496 | Execution halted
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diff changeset
497 |
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diff changeset
498 --------------------------------------
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diff changeset
499 | 4 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME)
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
500 | Dataset Blurb:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
501 | error
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
502 | Dataset Info:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
503 | PACKAGE INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
504 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
505 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
506 | Biobase 2.28.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
507 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
508 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
509 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
510 | igraph 0.7.1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
511 | xcms 1.44.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
512 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
513 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
514 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
515 | batch 1.1.4
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
516 | ARGUMENTS INFO
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lecorguille
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diff changeset
517 | xfunction annotatediff
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lecorguille
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518 | image /tmp/714467.1.short.q/tmpR_swdX
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diff changeset
519 | Dataset Job Standard Output:
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520 | PACKAGE INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
521 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
522 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
523 | Biobase 2.28.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
524 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
525 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
526 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
527 | igraph 0.7.1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
528 | xcms 1.44.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
529 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
530 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
531 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
532 | batch 1.1.4
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
533 | ARGUMENTS INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
534 | xfunction annotatediff
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lecorguille
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diff changeset
535 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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diff changeset
536 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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537 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
538 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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diff changeset
539 | convert_param FALSE
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diff changeset
540 | num_digits 0
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diff changeset
541 | nSlaves 1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
542 | sigma 6
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
543 | perfwhm 0.6
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diff changeset
544 | maxcharge 3
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diff changeset
545 | maxiso 4
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
546 | minfrac 0.5
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diff changeset
547 | ppm 5
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548 | mzabs 0.015
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
549 | intval into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
550 | max_peaks 100
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
551 | quick FALSE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
552 | polarity negative
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
553 | cor_eic_th 0.75
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
554 | graphMethod hcs
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
555 | pval 0.05
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
556 | calcCiS TRUE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
557 | calcIso FALSE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
558 | calcCaS FALSE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
559 | multiplier 3
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diff changeset
560 | runDiffreport TRUE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
561 | eicmax 200
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diff changeset
562 | eicwidth 200
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563 | value into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
564 | sortpval FALSE
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
565 | h 480
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566 | w 640
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diff changeset
567 | mzdec 2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
568 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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lecorguille
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569 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
570 | INFILE PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
571 | ARGUMENTS PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
572 | MAIN PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
573 | Start grouping after retention time.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
574 | Created 1566 pseudospectra.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
575 | Generating peak matrix!
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
576 | Run isotope peak annotation
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
577 | % finished: 10 20 30 40 50 60 70 80 90 100
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
578 | Found isotopes: 243
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
579 | Start grouping after correlation.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
580 | Generating EIC's ..
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
581 | Dataset Job Standard Error:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
582 | Fatal error: Exit code 1 ()
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
583 | Error in getAllPeakEICs(object, index = index) :
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
584 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
585 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
586 | Execution halted
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lecorguille
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diff changeset
587 |
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588 --------------------------------------
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
589 | 5 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME)
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
590 | Dataset Blurb:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
591 | error
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
592 | Dataset Info:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
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593 | PACKAGE INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
594 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
595 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
596 | Biobase 2.28.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
597 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
598 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
599 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
600 | igraph 0.7.1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
601 | xcms 1.44.0
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lecorguille
parents: 12
diff changeset
602 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
603 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
604 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
605 | batch 1.1.4
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
606 | ARGUMENTS INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
607 | xfunction annotatediff
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608 | image /tmp/714467.1.short.q/tmpR_swdX
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609 | Dataset Job Standard Output:
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610 | PACKAGE INFO
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611 | parallel 3.1.2
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612 | BiocGenerics 0.14.0
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613 | Biobase 2.28.0
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614 | Rcpp 0.12.0
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615 | mzR 2.2.2
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616 | tcltk 3.1.2
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617 | igraph 0.7.1
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618 | xcms 1.44.0
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619 | snow 0.3.13
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620 | CAMERA 1.22.0
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621 | multtest 2.22.0
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622 | batch 1.1.4
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623 | ARGUMENTS INFO
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624 | xfunction annotatediff
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625 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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626 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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627 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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628 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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629 | convert_param FALSE
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630 | num_digits 0
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631 | nSlaves 1
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632 | sigma 6
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633 | perfwhm 0.6
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634 | maxcharge 3
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635 | maxiso 4
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636 | minfrac 0.5
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637 | ppm 5
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638 | mzabs 0.015
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639 | intval into
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640 | max_peaks 100
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641 | quick FALSE
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642 | polarity negative
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643 | cor_eic_th 0.75
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644 | graphMethod hcs
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645 | pval 0.05
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646 | calcCiS TRUE
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647 | calcIso FALSE
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648 | calcCaS FALSE
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649 | multiplier 3
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650 | runDiffreport TRUE
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651 | eicmax 200
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652 | eicwidth 200
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653 | value into
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654 | sortpval FALSE
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655 | h 480
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656 | w 640
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657 | mzdec 2
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658 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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659 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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660 | INFILE PROCESSING INFO
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661 | ARGUMENTS PROCESSING INFO
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662 | MAIN PROCESSING INFO
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663 | Start grouping after retention time.
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664 | Created 1566 pseudospectra.
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665 | Generating peak matrix!
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666 | Run isotope peak annotation
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667 | % finished: 10 20 30 40 50 60 70 80 90 100
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668 | Found isotopes: 243
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669 | Start grouping after correlation.
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670 | Generating EIC's ..
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671 | Dataset Job Standard Error:
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672 | Fatal error: Exit code 1 ()
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673 | Error in getAllPeakEICs(object, index = index) :
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674 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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675 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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676 | Execution halted
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677 |
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678 --------------------------------------
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679 | 6 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME)
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680 | Dataset Blurb:
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681 | error
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682 | Dataset Info:
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683 | PACKAGE INFO
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684 | parallel 3.1.2
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685 | BiocGenerics 0.14.0
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686 | Biobase 2.28.0
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687 | Rcpp 0.12.0
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688 | mzR 2.2.2
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689 | tcltk 3.1.2
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690 | igraph 0.7.1
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691 | xcms 1.44.0
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692 | snow 0.3.13
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693 | CAMERA 1.22.0
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694 | multtest 2.22.0
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695 | batch 1.1.4
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696 | ARGUMENTS INFO
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697 | xfunction annotatediff
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698 | image /tmp/714467.1.short.q/tmpR_swdX
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699 | Dataset Job Standard Output:
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700 | PACKAGE INFO
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701 | parallel 3.1.2
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702 | BiocGenerics 0.14.0
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703 | Biobase 2.28.0
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704 | Rcpp 0.12.0
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705 | mzR 2.2.2
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706 | tcltk 3.1.2
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707 | igraph 0.7.1
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708 | xcms 1.44.0
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709 | snow 0.3.13
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710 | CAMERA 1.22.0
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711 | multtest 2.22.0
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712 | batch 1.1.4
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713 | ARGUMENTS INFO
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714 | xfunction annotatediff
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715 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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716 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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717 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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718 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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719 | convert_param FALSE
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720 | num_digits 0
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721 | nSlaves 1
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722 | sigma 6
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723 | perfwhm 0.6
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724 | maxcharge 3
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725 | maxiso 4
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726 | minfrac 0.5
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727 | ppm 5
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728 | mzabs 0.015
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729 | intval into
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730 | max_peaks 100
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731 | quick FALSE
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732 | polarity negative
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733 | cor_eic_th 0.75
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734 | graphMethod hcs
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735 | pval 0.05
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diff changeset
736 | calcCiS TRUE
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lecorguille
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diff changeset
737 | calcIso FALSE
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diff changeset
738 | calcCaS FALSE
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lecorguille
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diff changeset
739 | multiplier 3
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lecorguille
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diff changeset
740 | runDiffreport TRUE
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diff changeset
741 | eicmax 200
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diff changeset
742 | eicwidth 200
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diff changeset
743 | value into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
744 | sortpval FALSE
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lecorguille
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diff changeset
745 | h 480
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diff changeset
746 | w 640
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lecorguille
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diff changeset
747 | mzdec 2
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lecorguille
parents: 12
diff changeset
748 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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lecorguille
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diff changeset
749 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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lecorguille
parents: 12
diff changeset
750 | INFILE PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
751 | ARGUMENTS PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
752 | MAIN PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
753 | Start grouping after retention time.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
754 | Created 1566 pseudospectra.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
755 | Generating peak matrix!
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
756 | Run isotope peak annotation
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
757 | % finished: 10 20 30 40 50 60 70 80 90 100
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
758 | Found isotopes: 243
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lecorguille
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diff changeset
759 | Start grouping after correlation.
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diff changeset
760 | Generating EIC's ..
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lecorguille
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diff changeset
761 | Dataset Job Standard Error:
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diff changeset
762 | Fatal error: Exit code 1 ()
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diff changeset
763 | Error in getAllPeakEICs(object, index = index) :
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lecorguille
parents: 12
diff changeset
764 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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lecorguille
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diff changeset
765 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
766 | Execution halted
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diff changeset
767 |
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diff changeset
768 --------------------------------------
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lecorguille
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diff changeset
769 History with id 2891970512fa2d5a in error - summary of datasets in error below.
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lecorguille
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diff changeset
770 --------------------------------------
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lecorguille
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diff changeset
771 | 3 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME)
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
772 | Dataset Blurb:
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lecorguille
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diff changeset
773 | error
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
774 | Dataset Info:
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lecorguille
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diff changeset
775 | PACKAGE INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
776 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
777 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
778 | Biobase 2.28.0
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lecorguille
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diff changeset
779 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
780 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
781 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
782 | igraph 0.7.1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
783 | xcms 1.44.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
784 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
785 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
786 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
787 | batch 1.1.4
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lecorguille
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diff changeset
788 | ARGUMENTS INFO
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diff changeset
789 | xfunction annotatediff
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diff changeset
790 | image /tmp/714467.1.short.q/tmpR_swdX
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diff changeset
791 | Dataset Job Standard Output:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
792 | PACKAGE INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
793 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
794 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
795 | Biobase 2.28.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
796 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
797 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
798 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
799 | igraph 0.7.1
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
800 | xcms 1.44.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
801 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
802 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
803 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
804 | batch 1.1.4
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diff changeset
805 | ARGUMENTS INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
806 | xfunction annotatediff
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diff changeset
807 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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lecorguille
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diff changeset
808 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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lecorguille
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diff changeset
809 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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lecorguille
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diff changeset
810 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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diff changeset
811 | convert_param FALSE
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diff changeset
812 | num_digits 0
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diff changeset
813 | nSlaves 1
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diff changeset
814 | sigma 6
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diff changeset
815 | perfwhm 0.6
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diff changeset
816 | maxcharge 3
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diff changeset
817 | maxiso 4
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diff changeset
818 | minfrac 0.5
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diff changeset
819 | ppm 5
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diff changeset
820 | mzabs 0.015
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
821 | intval into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
822 | max_peaks 100
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diff changeset
823 | quick FALSE
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diff changeset
824 | polarity negative
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
825 | cor_eic_th 0.75
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diff changeset
826 | graphMethod hcs
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diff changeset
827 | pval 0.05
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diff changeset
828 | calcCiS TRUE
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diff changeset
829 | calcIso FALSE
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diff changeset
830 | calcCaS FALSE
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lecorguille
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diff changeset
831 | multiplier 3
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lecorguille
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diff changeset
832 | runDiffreport TRUE
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lecorguille
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diff changeset
833 | eicmax 200
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834 | eicwidth 200
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diff changeset
835 | value into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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836 | sortpval FALSE
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diff changeset
837 | h 480
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diff changeset
838 | w 640
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diff changeset
839 | mzdec 2
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diff changeset
840 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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841 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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diff changeset
842 | INFILE PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
843 | ARGUMENTS PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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844 | MAIN PROCESSING INFO
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
845 | Start grouping after retention time.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
846 | Created 1566 pseudospectra.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
847 | Generating peak matrix!
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
848 | Run isotope peak annotation
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849 | % finished: 10 20 30 40 50 60 70 80 90 100
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diff changeset
850 | Found isotopes: 243
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
851 | Start grouping after correlation.
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
852 | Generating EIC's ..
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 12
diff changeset
853 | Dataset Job Standard Error:
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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854 | Fatal error: Exit code 1 ()
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855 | Error in getAllPeakEICs(object, index = index) :
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lecorguille
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diff changeset
856 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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lecorguille
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diff changeset
857 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
858 | Execution halted
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859 |
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860 --------------------------------------
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861 | 4 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME)
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diff changeset
862 | Dataset Blurb:
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863 | error
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864 | Dataset Info:
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865 | PACKAGE INFO
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866 | parallel 3.1.2
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867 | BiocGenerics 0.14.0
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868 | Biobase 2.28.0
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869 | Rcpp 0.12.0
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diff changeset
870 | mzR 2.2.2
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871 | tcltk 3.1.2
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872 | igraph 0.7.1
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873 | xcms 1.44.0
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874 | snow 0.3.13
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875 | CAMERA 1.22.0
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876 | multtest 2.22.0
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877 | batch 1.1.4
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878 | ARGUMENTS INFO
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879 | xfunction annotatediff
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880 | image /tmp/714467.1.short.q/tmpR_swdX
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diff changeset
881 | Dataset Job Standard Output:
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882 | PACKAGE INFO
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diff changeset
883 | parallel 3.1.2
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diff changeset
884 | BiocGenerics 0.14.0
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diff changeset
885 | Biobase 2.28.0
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diff changeset
886 | Rcpp 0.12.0
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diff changeset
887 | mzR 2.2.2
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diff changeset
888 | tcltk 3.1.2
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diff changeset
889 | igraph 0.7.1
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diff changeset
890 | xcms 1.44.0
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diff changeset
891 | snow 0.3.13
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diff changeset
892 | CAMERA 1.22.0
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diff changeset
893 | multtest 2.22.0
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894 | batch 1.1.4
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diff changeset
895 | ARGUMENTS INFO
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diff changeset
896 | xfunction annotatediff
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897 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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diff changeset
898 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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diff changeset
899 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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diff changeset
900 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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901 | convert_param FALSE
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902 | num_digits 0
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903 | nSlaves 1
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904 | sigma 6
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diff changeset
905 | perfwhm 0.6
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diff changeset
906 | maxcharge 3
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diff changeset
907 | maxiso 4
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diff changeset
908 | minfrac 0.5
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diff changeset
909 | ppm 5
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diff changeset
910 | mzabs 0.015
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diff changeset
911 | intval into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
912 | max_peaks 100
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diff changeset
913 | quick FALSE
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diff changeset
914 | polarity negative
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diff changeset
915 | cor_eic_th 0.75
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diff changeset
916 | graphMethod hcs
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diff changeset
917 | pval 0.05
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918 | calcCiS TRUE
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diff changeset
919 | calcIso FALSE
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diff changeset
920 | calcCaS FALSE
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diff changeset
921 | multiplier 3
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922 | runDiffreport TRUE
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diff changeset
923 | eicmax 200
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924 | eicwidth 200
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diff changeset
925 | value into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
926 | sortpval FALSE
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diff changeset
927 | h 480
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928 | w 640
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929 | mzdec 2
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diff changeset
930 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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931 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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932 | INFILE PROCESSING INFO
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diff changeset
933 | ARGUMENTS PROCESSING INFO
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diff changeset
934 | MAIN PROCESSING INFO
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935 | Start grouping after retention time.
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936 | Created 1566 pseudospectra.
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diff changeset
937 | Generating peak matrix!
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diff changeset
938 | Run isotope peak annotation
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939 | % finished: 10 20 30 40 50 60 70 80 90 100
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diff changeset
940 | Found isotopes: 243
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diff changeset
941 | Start grouping after correlation.
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942 | Generating EIC's ..
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diff changeset
943 | Dataset Job Standard Error:
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944 | Fatal error: Exit code 1 ()
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945 | Error in getAllPeakEICs(object, index = index) :
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diff changeset
946 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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diff changeset
947 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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diff changeset
948 | Execution halted
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949 |
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950 --------------------------------------
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951 | 5 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME)
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
952 | Dataset Blurb:
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953 | error
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954 | Dataset Info:
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955 | PACKAGE INFO
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956 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
957 | BiocGenerics 0.14.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
958 | Biobase 2.28.0
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diff changeset
959 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
960 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
961 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
962 | igraph 0.7.1
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diff changeset
963 | xcms 1.44.0
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diff changeset
964 | snow 0.3.13
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diff changeset
965 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
966 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
967 | batch 1.1.4
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968 | ARGUMENTS INFO
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969 | xfunction annotatediff
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970 | image /tmp/714467.1.short.q/tmpR_swdX
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971 | Dataset Job Standard Output:
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972 | PACKAGE INFO
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973 | parallel 3.1.2
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diff changeset
974 | BiocGenerics 0.14.0
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975 | Biobase 2.28.0
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976 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
977 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
978 | tcltk 3.1.2
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diff changeset
979 | igraph 0.7.1
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diff changeset
980 | xcms 1.44.0
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diff changeset
981 | snow 0.3.13
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diff changeset
982 | CAMERA 1.22.0
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diff changeset
983 | multtest 2.22.0
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diff changeset
984 | batch 1.1.4
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985 | ARGUMENTS INFO
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986 | xfunction annotatediff
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987 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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988 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
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989 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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990 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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991 | convert_param FALSE
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992 | num_digits 0
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993 | nSlaves 1
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diff changeset
994 | sigma 6
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995 | perfwhm 0.6
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diff changeset
996 | maxcharge 3
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diff changeset
997 | maxiso 4
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998 | minfrac 0.5
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diff changeset
999 | ppm 5
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1000 | mzabs 0.015
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1001 | intval into
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diff changeset
1002 | max_peaks 100
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diff changeset
1003 | quick FALSE
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diff changeset
1004 | polarity negative
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diff changeset
1005 | cor_eic_th 0.75
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1006 | graphMethod hcs
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diff changeset
1007 | pval 0.05
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1008 | calcCiS TRUE
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1009 | calcIso FALSE
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diff changeset
1010 | calcCaS FALSE
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diff changeset
1011 | multiplier 3
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1012 | runDiffreport TRUE
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1013 | eicmax 200
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1014 | eicwidth 200
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1015 | value into
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1016 | sortpval FALSE
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1017 | h 480
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1018 | w 640
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diff changeset
1019 | mzdec 2
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diff changeset
1020 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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1021 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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1022 | INFILE PROCESSING INFO
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diff changeset
1023 | ARGUMENTS PROCESSING INFO
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diff changeset
1024 | MAIN PROCESSING INFO
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1025 | Start grouping after retention time.
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diff changeset
1026 | Created 1566 pseudospectra.
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diff changeset
1027 | Generating peak matrix!
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diff changeset
1028 | Run isotope peak annotation
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diff changeset
1029 | % finished: 10 20 30 40 50 60 70 80 90 100
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1030 | Found isotopes: 243
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diff changeset
1031 | Start grouping after correlation.
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diff changeset
1032 | Generating EIC's ..
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1033 | Dataset Job Standard Error:
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1034 | Fatal error: Exit code 1 ()
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diff changeset
1035 | Error in getAllPeakEICs(object, index = index) :
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lecorguille
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diff changeset
1036 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1037 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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diff changeset
1038 | Execution halted
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diff changeset
1039 |
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diff changeset
1040 --------------------------------------
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1041 | 6 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME)
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diff changeset
1042 | Dataset Blurb:
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diff changeset
1043 | error
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diff changeset
1044 | Dataset Info:
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diff changeset
1045 | PACKAGE INFO
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diff changeset
1046 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
1047 | BiocGenerics 0.14.0
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lecorguille
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diff changeset
1048 | Biobase 2.28.0
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lecorguille
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diff changeset
1049 | Rcpp 0.12.0
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diff changeset
1050 | mzR 2.2.2
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diff changeset
1051 | tcltk 3.1.2
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lecorguille
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diff changeset
1052 | igraph 0.7.1
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diff changeset
1053 | xcms 1.44.0
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diff changeset
1054 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1055 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1056 | multtest 2.22.0
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diff changeset
1057 | batch 1.1.4
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diff changeset
1058 | ARGUMENTS INFO
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1059 | xfunction annotatediff
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diff changeset
1060 | image /tmp/714467.1.short.q/tmpR_swdX
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1061 | Dataset Job Standard Output:
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diff changeset
1062 | PACKAGE INFO
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diff changeset
1063 | parallel 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1064 | BiocGenerics 0.14.0
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lecorguille
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diff changeset
1065 | Biobase 2.28.0
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lecorguille
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diff changeset
1066 | Rcpp 0.12.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1067 | mzR 2.2.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1068 | tcltk 3.1.2
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
1069 | igraph 0.7.1
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diff changeset
1070 | xcms 1.44.0
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diff changeset
1071 | snow 0.3.13
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1072 | CAMERA 1.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1073 | multtest 2.22.0
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
1074 | batch 1.1.4
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diff changeset
1075 | ARGUMENTS INFO
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diff changeset
1076 | xfunction annotatediff
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diff changeset
1077 | image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat
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lecorguille
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diff changeset
1078 | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
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diff changeset
1079 | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat
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lecorguille
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1080 | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat
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lecorguille
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diff changeset
1081 | convert_param FALSE
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lecorguille
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diff changeset
1082 | num_digits 0
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1083 | nSlaves 1
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1084 | sigma 6
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diff changeset
1085 | perfwhm 0.6
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diff changeset
1086 | maxcharge 3
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diff changeset
1087 | maxiso 4
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diff changeset
1088 | minfrac 0.5
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diff changeset
1089 | ppm 5
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diff changeset
1090 | mzabs 0.015
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diff changeset
1091 | intval into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1092 | max_peaks 100
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diff changeset
1093 | quick FALSE
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1094 | polarity negative
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diff changeset
1095 | cor_eic_th 0.75
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diff changeset
1096 | graphMethod hcs
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diff changeset
1097 | pval 0.05
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diff changeset
1098 | calcCiS TRUE
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diff changeset
1099 | calcIso FALSE
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diff changeset
1100 | calcCaS FALSE
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diff changeset
1101 | multiplier 3
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1102 | runDiffreport TRUE
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1103 | eicmax 200
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1104 | eicwidth 200
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1105 | value into
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1106 | sortpval FALSE
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1107 | h 480
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diff changeset
1108 | w 640
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1109 | mzdec 2
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1110 | new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_
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1111 | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat
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1112 | INFILE PROCESSING INFO
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1113 | ARGUMENTS PROCESSING INFO
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1114 | MAIN PROCESSING INFO
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1115 | Start grouping after retention time.
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1116 | Created 1566 pseudospectra.
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1117 | Generating peak matrix!
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1118 | Run isotope peak annotation
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1119 | % finished: 10 20 30 40 50 60 70 80 90 100
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1120 | Found isotopes: 243
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1121 | Start grouping after correlation.
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1122 | Generating EIC's ..
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1123 | Dataset Job Standard Error:
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1124 | Fatal error: Exit code 1 ()
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1125 | Error in getAllPeakEICs(object, index = index) :
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1126 | Raw data file:sacuri/bio/HU_neg_017.mzXML not found !
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1127 | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
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1128 | Execution halted
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1129 |
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1130 --------------------------------------
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1131
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1132 --------------------- >> end captured stdout << ----------------------
10
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1133 -------------------- >> begin captured logging << --------------------
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1134 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1135 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
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1136 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None
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1137 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1138 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
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1139 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None
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1140 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1141 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
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1142 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
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1143 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1144 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None
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1145 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1146 galaxy.tools: DEBUG: Validated and populated state for tool request (47.490 ms)
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1147 galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.544 ms)
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1148 galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (391.258 ms)
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1149 galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
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1150 galaxy.tools.actions.upload: DEBUG: Created upload job (273.829 ms)
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1151 galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (686.205 ms)
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1152 galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (727.583 ms)
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1153 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
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1154 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1155 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1156 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1157 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1158 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1159 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1160 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1161 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1162 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1163 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1164 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1165 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1166 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1167 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1168 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1169 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1170 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1171 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1172 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1173 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1174 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1175 galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1
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1176 galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner
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1177 galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
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1178 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1179 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1180 galaxy.jobs.runners: DEBUG: Job [1] queued (154.781 ms)
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1181 galaxy.jobs.handler: INFO: (1) Job dispatched
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1182 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1183 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1184 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1185 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1186 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
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1187 galaxy.tools.deps: DEBUG: Find dependency samtools version None
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1188 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1189 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1190 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1191 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1192 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1193 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
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1194 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1195 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1196 galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/tools/data_source/upload.py /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpyH3qpG 1:/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/dataset_1_files:/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat]
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1197 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1198 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1199 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1200 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1201 galaxy.jobs.runners: DEBUG: (1) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/set_metadata_eD8s7d.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_jShRti,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_oFrnPD,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_BhnvZW,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_Een9yT,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_R_kK3g" 5242880; sh -c "exit $return_code"
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1202 galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/galaxy_1.sh
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1203 galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
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1204 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1205 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1206 galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/galaxy_1.sh
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1207 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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diff changeset
1208 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1209 galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1
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1210 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1211 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1212 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
12
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1213 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1214 galaxy.jobs: DEBUG: job 1 ended (finish() executed in (836.273 ms))
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1215 galaxy.tools: DEBUG: Validated and populated state for tool request (44.879 ms)
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1216 galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.644 ms)
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1217 galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (508.110 ms)
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1218 galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2
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1219 galaxy.tools.actions.upload: DEBUG: Created upload job (216.184 ms)
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1220 galaxy.tools.execute: DEBUG: Tool [upload1] created job [2] (745.459 ms)
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1221 galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (787.748 ms)
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1222 galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2
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1223 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
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1224 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1225 galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner
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1226 galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
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1227 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1228 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1229 galaxy.jobs.runners: DEBUG: Job [2] queued (142.382 ms)
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1230 galaxy.jobs.handler: INFO: (2) Job dispatched
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1231 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1232 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1233 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1234 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1235 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
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1236 galaxy.tools.deps: DEBUG: Find dependency samtools version None
13
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1237 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1238 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1239 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1240 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1241 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
10
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1242 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
13
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1243 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1244 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1245 galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/tools/data_source/upload.py /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpxnh06b 2:/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/dataset_2_files:/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat]
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diff changeset
1246 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
11
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1247 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1248 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1249 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1250 galaxy.jobs.runners: DEBUG: (2) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/set_metadata_s1bC30.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_4VZIsA,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_8kyCYN,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_Wr01BS,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_8aeiqq,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2__DjwYh" 5242880; sh -c "exit $return_code"
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1251 galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/galaxy_2.sh
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1252 galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
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diff changeset
1253 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
12
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1254 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1255 galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/galaxy_2.sh
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1256 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1257 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1258 galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2
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1259 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
12
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1260 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1261 galaxy.tools: DEBUG: Validated and populated state for tool request (73.689 ms)
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1262 galaxy.tools.actions: INFO: Handled output named variableMetadata for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (110.026 ms)
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1263 galaxy.jobs: DEBUG: job 2 ended (finish() executed in (767.672 ms))
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1264 galaxy.tools.actions: INFO: Handled output named datamatrix for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (138.821 ms)
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1265 galaxy.tools.actions: INFO: Handled output named rdata for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (94.946 ms)
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1266 galaxy.tools.actions: INFO: Handled output named output_diffreport for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (109.181 ms)
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1267 galaxy.tools.actions: INFO: Added output datasets to history (62.241 ms)
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1268 galaxy.tools.actions: INFO: Verified access to datasets for Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] (25.832 ms)
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1269 galaxy.tools.actions: INFO: Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] complete, ready to flush (70.198 ms)
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1270 galaxy.tools.actions: INFO: Flushed transaction for job Job[id=3,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] (98.006 ms)
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1271 galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [3] (695.936 ms)
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1272 galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 request: (734.968 ms)
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1273 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
12
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1274 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1275 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
12
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1276 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1277 galaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3
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1278 galaxy.jobs.handler: DEBUG: (3) Dispatching to local runner
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1279 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1280 galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)
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1281 galaxy.jobs.runners: DEBUG: Job [3] queued (127.546 ms)
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1282 galaxy.jobs.handler: INFO: (3) Job dispatched
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1283 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1284 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'R'
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1285 galaxy.tools.deps: DEBUG: Find dependency R version 3.1.2
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1286 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b67c021cd90> (isnull? False)
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1287 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-snow'
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1288 galaxy.tools.deps: DEBUG: Find dependency r-snow version 0.4_1
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1289 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1290 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1291 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1292 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1293 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1294 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-snow', ignoring
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1295 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'bioconductor-camera'
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1296 galaxy.tools.deps: DEBUG: Find dependency bioconductor-camera version 1.22.0
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1297 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b67c021cd10> (isnull? False)
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1298 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-batch'
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1299 galaxy.tools.deps: DEBUG: Find dependency r-batch version 1.1_4
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1300 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1301 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1302 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1303 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1304 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True)
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1305 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-batch', ignoring
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1306 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'graphicsmagick'
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1307 galaxy.tools.deps: DEBUG: Find dependency graphicsmagick version 1.3.20
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1308 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b67c021cf10> (isnull? False)
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1309 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1310 galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/R/3.1.2/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/R/3.1.2/lecorguille/camera_annotate/db270f704d93/env.sh; PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/db270f704d93/env.sh; PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/db270f704d93/env.sh; LANG=C Rscript /tmp/714467.1.short.q/tmpR_swdX/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/db270f704d93/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_ zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat]
12
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1311 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1312 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1313 galaxy.jobs.runners: DEBUG: (3) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/set_metadata_Xzws5e.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_cUhbAk,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_32gPgn,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_dAG7BN,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_wm2Akf,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_aw4Xwc" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_4_YmkXG2,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_4_M9NNV9,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_4_FSIoJm,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_4_rc0u_S,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_4_RAjtyp" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_5_2db6tk,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_5_MSmEkX,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_5_WtSkOw,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_5_zt5c5k,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_5_n4DVAW" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_6_wxbF7c,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_6_HXczlo,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_6_U8R0i3,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_6_ZxcRT0,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_6.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_6_Kf06sK" 5242880; sh -c "exit $return_code"
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1314 galaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/galaxy_3.sh
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1315 galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)
12
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1316 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
13
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1317 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1318 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1319 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1320 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1321 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1322 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1323 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1324 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1325 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1326 galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/galaxy_3.sh
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1327 galaxy.jobs.output_checker: INFO: Job 3: Fatal error: Exit code 1 ()
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1328 galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job.
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1329 galaxy.jobs: DEBUG: (3) setting dataset 3 state to ERROR
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1330 galaxy.jobs: DEBUG: (3) setting dataset 4 state to ERROR
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1331 galaxy.jobs: DEBUG: (3) setting dataset 5 state to ERROR
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1332 galaxy.jobs: DEBUG: (3) setting dataset 6 state to ERROR
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1333 galaxy.jobs: DEBUG: job 3 ended (finish() executed in (632.872 ms))
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1334 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1335 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1336 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1337 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1338 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1339 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1340 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1341 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1342 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1343 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1344 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1345 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1346 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1347 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1348 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1349 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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diff changeset
1350 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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diff changeset
1351 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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diff changeset
1352 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1353 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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diff changeset
1354 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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diff changeset
1355 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?full=true&key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1356 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1357 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1358 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1359 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1360 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1361 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1362 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1363 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1364 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1365 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1366 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1367 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1368 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1369 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1370 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1371 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1372 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1373 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1374 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1375 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1376 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1377 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1378 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1379 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1380 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1381 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1382 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
ba7db5b70639 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
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1383 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1384 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1385 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1386 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1387 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1388 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1389 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1390 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1391 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1392 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1393 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1394 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
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1395 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None
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1396 --------------------- >> end captured logging << ---------------------
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1397
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1398 ----------------------------------------------------------------------
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1399 XML: /tmp/714467.1.short.q/tmpR_swdX/xunit.xml
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1400 ----------------------------------------------------------------------
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1401 Ran 1 test in 123.315s
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1402
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1403 FAILED (failures=1)
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1404 cp: cannot stat `/tmp/714467.1.short.q/tmpR_swdX/jobfiles/*': No such file or directory
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1405 There were problems with 1 test(s) - out of 1 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.