Mercurial > repos > iuc > rgrnastar
view test-data/test-cache/tophat-test/Log.out @ 16:e132e7d02a3e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
| author | iuc |
|---|---|
| date | Fri, 04 Dec 2020 22:05:07 +0000 |
| parents | 5ec75f5dae3c |
| children |
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STAR version=2.7.5a STAR compilation time,server,dir=Tue Jun 16 12:17:16 EDT 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source ##### Command Line: STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate ~RE-DEFINED genomeDir tempstargenomedir ~RE-DEFINED genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa ~RE-DEFINED genomeSAindexNbases 5 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate genomeDir tempstargenomedir genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa genomeSAindexNbases 5 ------------------------------- ##### Final effective command line: STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 ---------------------------------------- Number of fastq files for each mate = 1 Finished loading and checking parameters --genomeDir directory created: tempstargenomedir/ Jul 29 17:04:16 ... starting to generate Genome files tools/rgrnastar/test-data/tophat_test.fa : chr # 0 "test_chromosome" chrStart: 0 Estimated genome size=201262144 = 262144 + 201000000 GstrandBit=32 Number of SA indices: 1300 Jul 29 17:04:16 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 1; chunks size limit: 18599685304 bytes Jul 29 17:04:16 ... sorting Suffix Array chunks and saving them to disk... Writing 10400 bytes into tempstargenomedir//SA_0 ; empty space on disk = 66320359424 bytes ... done Jul 29 17:04:16 ... loading chunks from disk, packing SA... Jul 29 17:04:16 ... finished generating suffix array Jul 29 17:04:16 ... generating Suffix Array index Jul 29 17:04:16 ... completed Suffix Array index Jul 29 17:04:16 ... writing Genome to disk ... Writing 262144 bytes into tempstargenomedir//Genome ; empty space on disk = 66320355328 bytes ... done SA size in bytes: 5366 Jul 29 17:04:16 ... writing Suffix Array to disk ... Writing 5366 bytes into tempstargenomedir//SA ; empty space on disk = 66320093184 bytes ... done Jul 29 17:04:16 ... writing SAindex to disk Writing 8 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done Writing 48 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done Writing 5971 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done Jul 29 17:04:16 ..... finished successfully DONE: Genome generation, EXITING