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annotate libs/sratoolkit.2.8.0-centos_linux64/README-blastn @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 # ===========================================================================
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2 #
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3 # PUBLIC DOMAIN NOTICE
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4 # National Center for Biotechnology Information
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5 #
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6 # This software/database is a "United States Government Work" under the
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7 # terms of the United States Copyright Act. It was written as part of
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8 # the author's official duties as a United States Government employee and
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9 # thus cannot be copyrighted. This software/database is freely available
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10 # to the public for use. The National Library of Medicine and the U.S.
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11 # Government have not placed any restriction on its use or reproduction.
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12 #
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13 # Although all reasonable efforts have been taken to ensure the accuracy
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14 # and reliability of the software and data, the NLM and the U.S.
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15 # Government do not and cannot warrant the performance or results that
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16 # may be obtained by using this software or data. The NLM and the U.S.
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17 # Government disclaim all warranties, express or implied, including
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18 # warranties of performance, merchantability or fitness for any particular
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19 # purpose.
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20 #
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21 # Please cite the author in any work or product based on this material.
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22 #
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23 # ===========================================================================
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24
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25
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26 The NCBI SRA ( Sequence Read Archive )
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27
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28
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29 Contact: sra-tools@ncbi.nlm.nih.gov
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30 http://trace.ncbi.nlm.nih.gov/Traces/sra/std
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31
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32
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33 Stand-alone BLAST searches against SRA runs in their native format.
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34 -------------------------------------------------------------------
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35
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36 A stand-alone blastn application to perform BLAST searches directly against
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37 native SRA files is included in this distribution. This application has been
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38 tested in-house at the NCBI, but has not been heavily used, so this should be
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39 considered a preliminary (alpha) release to a few experienced users. A 64-bit
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40 LINUX application has been built for this testing.
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41
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42 The application is called "blastn_vdb".
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43
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44 The application can be invoked in much the same manner as the standard
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45 blastn application:
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46
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47 1) blastn_vdb -help or blastn_vdb -h will produce usage messages.
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48
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49 2) The BLAST+ command-line manual at http://www.ncbi.nlm.nih.gov/books/NBK1763/
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50 provides more details on the options, though not all blastn options are
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51 available with blastn_vdb. Some options simply do not apply to sequences in SRA
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52 (e.g., -gilist is missing as these sequences have not been assigned GI's). Some
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53 options have not yet been implemented (e.g., -num_threads is currently disabled).
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54
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55
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56 To search cached or on-demand SRA objects.
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57 ------------------------------------------
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58 An example blastn_vdb command-line would be:
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59
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60 ./blastn_vdb -db "ERR039542 ERR047215 ERR039539 ERR039540" -query nt.test -out test.out
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61
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62 The file nt.test contains the query in FASTA format, and it will be searched against
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63 the reads in runs with accessions ERR039542 ERR047215 ERR039539 ERR039540.
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64
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65 If you have not already downloaded these objects using the vdb "prefetch" tool,
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66 they will be retrieved on-demand from NCBI under standard configuration. For
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67 alternative configuration information, please see the "README-vdb-config" file
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68 in this distribution.
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69
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70 Searching with manually downloaded files.
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71 -----------------------------------------
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72 If you have manually downloaded files, e.g. via aspera or wget, etc., they may
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73 be referred to as "local" files. You can pass one or more file paths to be used
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74 collectively as the database. In this case the blastn_vdb command-line would be:
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75
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76 ./blastn_vdb -db <SRR_file> -query <input_file> -out <output_file>
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77
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78 Where
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79 <SRR_file> is the path (relative or absolute) and name of the SRRxxxxx file
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80 <input_file> is a fasta file containing the sequence(s) to be BLASTed
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81 <output_file> is the name specified for the output report of the blast search.
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82
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83 Example:
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84
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85 ./blastn_vdb -db ./subdir/ERR039542.sra -query nt.test -out test.out
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86
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87 Querying multiple SRR files simultaneously:
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88
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89 ./blastn_vdb -db "<SRR_file1> <SRR_file2> <SRR_file3>" -query <input.fa> -out <output_file>
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90
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91 Enclose the group of files to be included in the search set in "quotes", e.g.
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92 "./SRR_file1.sra ./SRR_file2.sra ./SRR_file3.sra"
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93
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94 Example:
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95
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96 ./blastn_vdb -db "./ERR039542.sra ./ERR047215.sra ./ERR039539.sra ./ERR039540.sra" -query nt.test -out test.out
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97
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98 Caveats
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99 -------
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100 There are some limitations on the currently available application:
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101
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102 1) Individual SRA data files containing more than 2 billion reads are not yet supported. For a
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103 paired-end experiment this is actually a limitation of about 1 billion "spots".
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104
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105 2) Compressed SRA ("cSRA") is not yet fully supported. Currently, only the
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106 unaligned fraction of reads are searched. Compressed SRA are runs containing
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107 alignments (e.g., ERR230455). Runs can be checked with "vdb-dump" to report if
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108 they contain alignment information:
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109
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110 $ vdb-dump -E ERR230455
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111 enumerating the tables of database 'ERR230455'
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112 tbl #1: PRIMARY_ALIGNMENT
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113 tbl #2: REFERENCE
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114 tbl #3: SEQUENCE
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115
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116 3) You may need to prefix "./" to the run name for files in your current
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117 directory.
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118
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119 4) The blast_formatter is not currently able to read native SRA files, so
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120 reformatting of results saved as a blast archive is not yet supported.
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121
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122 Common errors and fixes.
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123 ------------------------
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124
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125 1) Failure to provide relative path to manually downloaded SRR file:
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126
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127 ./blastn_vdb -db SRR770754.sra -query srr770754_test.fa -out test.out
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128 Error: NCBI C++ Exception:
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129 "vdb2blast_util.cpp", line 253: Error: ncbi::CVDBBlastUtil::x_MakeSRASeqSrc()
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130 - VDB BlastSeqSrc construction failed: Failed to add any run to VDB runset: unsupported while allocating
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131
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132 Fix:
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133 Include relative (e.g., "../" or "./") or absolute (e.g., "/home/user/SRA_BLAST_data/") file path with SRR file