view test-data/test-cache/tophat-test/Log.out @ 17:5ef7ec16b04f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32

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

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##### Final effective command line:
STAR   --runMode genomeGenerate   --genomeDir tempstargenomedir   --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa      --genomeSAindexNbases 5
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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