Mercurial > repos > iuc > rgrnastar
diff test-data/test-cache/tophat-test/Log.out @ 15:5ec75f5dae3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
| author | iuc |
|---|---|
| date | Wed, 05 Aug 2020 09:40:33 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/Log.out Wed Aug 05 09:40:33 2020 -0400 @@ -0,0 +1,50 @@ +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