diff 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"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-cache/tophat-test/Log.out	Thu Jul 30 14:37:28 2020 +0000
@@ -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