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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
author dave
date Thu, 30 Jul 2020 14:37:28 +0000
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8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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1 STAR version=2.7.5a
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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2 STAR compilation time,server,dir=Tue Jun 16 12:17:16 EDT 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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3 ##### Command Line:
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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4 STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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5 ##### Initial USER parameters from Command Line:
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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6 ###### All USER parameters from Command Line:
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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7 runMode genomeGenerate ~RE-DEFINED
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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8 genomeDir tempstargenomedir ~RE-DEFINED
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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9 genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa ~RE-DEFINED
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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10 genomeSAindexNbases 5 ~RE-DEFINED
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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11 ##### Finished reading parameters from all sources
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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12
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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13 ##### Final user re-defined parameters-----------------:
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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14 runMode genomeGenerate
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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15 genomeDir tempstargenomedir
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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16 genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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17 genomeSAindexNbases 5
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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18
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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19 -------------------------------
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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20 ##### Final effective command line:
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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21 STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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22 ----------------------------------------
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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23
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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24 Number of fastq files for each mate = 1
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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25 Finished loading and checking parameters
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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26 --genomeDir directory created: tempstargenomedir/
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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27 Jul 29 17:04:16 ... starting to generate Genome files
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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28 tools/rgrnastar/test-data/tophat_test.fa : chr # 0 "test_chromosome" chrStart: 0
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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29 Estimated genome size=201262144 = 262144 + 201000000
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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30 GstrandBit=32
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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31 Number of SA indices: 1300
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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32 Jul 29 17:04:16 ... starting to sort Suffix Array. This may take a long time...
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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33 Number of chunks: 1; chunks size limit: 18599685304 bytes
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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34 Jul 29 17:04:16 ... sorting Suffix Array chunks and saving them to disk...
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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35 Writing 10400 bytes into tempstargenomedir//SA_0 ; empty space on disk = 66320359424 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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36 Jul 29 17:04:16 ... loading chunks from disk, packing SA...
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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37 Jul 29 17:04:16 ... finished generating suffix array
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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38 Jul 29 17:04:16 ... generating Suffix Array index
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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39 Jul 29 17:04:16 ... completed Suffix Array index
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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40 Jul 29 17:04:16 ... writing Genome to disk ...
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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41 Writing 262144 bytes into tempstargenomedir//Genome ; empty space on disk = 66320355328 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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42 SA size in bytes: 5366
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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43 Jul 29 17:04:16 ... writing Suffix Array to disk ...
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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44 Writing 5366 bytes into tempstargenomedir//SA ; empty space on disk = 66320093184 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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45 Jul 29 17:04:16 ... writing SAindex to disk
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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46 Writing 8 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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47 Writing 48 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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48 Writing 5971 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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49 Jul 29 17:04:16 ..... finished successfully
8ea3e134b4db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
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50 DONE: Genome generation, EXITING