Mercurial > repos > dave > rna_starsolo
comparison test-data/test-cache/tophat-test/Log.out @ 0:8ea3e134b4db draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
| author | dave |
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| date | Thu, 30 Jul 2020 14:37:28 +0000 |
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| children |
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| -1:000000000000 | 0:8ea3e134b4db |
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| 1 STAR version=2.7.5a | |
| 2 STAR compilation time,server,dir=Tue Jun 16 12:17:16 EDT 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source | |
| 3 ##### Command Line: | |
| 4 STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 | |
| 5 ##### Initial USER parameters from Command Line: | |
| 6 ###### All USER parameters from Command Line: | |
| 7 runMode genomeGenerate ~RE-DEFINED | |
| 8 genomeDir tempstargenomedir ~RE-DEFINED | |
| 9 genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa ~RE-DEFINED | |
| 10 genomeSAindexNbases 5 ~RE-DEFINED | |
| 11 ##### Finished reading parameters from all sources | |
| 12 | |
| 13 ##### Final user re-defined parameters-----------------: | |
| 14 runMode genomeGenerate | |
| 15 genomeDir tempstargenomedir | |
| 16 genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa | |
| 17 genomeSAindexNbases 5 | |
| 18 | |
| 19 ------------------------------- | |
| 20 ##### Final effective command line: | |
| 21 STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 | |
| 22 ---------------------------------------- | |
| 23 | |
| 24 Number of fastq files for each mate = 1 | |
| 25 Finished loading and checking parameters | |
| 26 --genomeDir directory created: tempstargenomedir/ | |
| 27 Jul 29 17:04:16 ... starting to generate Genome files | |
| 28 tools/rgrnastar/test-data/tophat_test.fa : chr # 0 "test_chromosome" chrStart: 0 | |
| 29 Estimated genome size=201262144 = 262144 + 201000000 | |
| 30 GstrandBit=32 | |
| 31 Number of SA indices: 1300 | |
| 32 Jul 29 17:04:16 ... starting to sort Suffix Array. This may take a long time... | |
| 33 Number of chunks: 1; chunks size limit: 18599685304 bytes | |
| 34 Jul 29 17:04:16 ... sorting Suffix Array chunks and saving them to disk... | |
| 35 Writing 10400 bytes into tempstargenomedir//SA_0 ; empty space on disk = 66320359424 bytes ... done | |
| 36 Jul 29 17:04:16 ... loading chunks from disk, packing SA... | |
| 37 Jul 29 17:04:16 ... finished generating suffix array | |
| 38 Jul 29 17:04:16 ... generating Suffix Array index | |
| 39 Jul 29 17:04:16 ... completed Suffix Array index | |
| 40 Jul 29 17:04:16 ... writing Genome to disk ... | |
| 41 Writing 262144 bytes into tempstargenomedir//Genome ; empty space on disk = 66320355328 bytes ... done | |
| 42 SA size in bytes: 5366 | |
| 43 Jul 29 17:04:16 ... writing Suffix Array to disk ... | |
| 44 Writing 5366 bytes into tempstargenomedir//SA ; empty space on disk = 66320093184 bytes ... done | |
| 45 Jul 29 17:04:16 ... writing SAindex to disk | |
| 46 Writing 8 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done | |
| 47 Writing 48 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done | |
| 48 Writing 5971 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done | |
| 49 Jul 29 17:04:16 ..... finished successfully | |
| 50 DONE: Genome generation, EXITING |