STAR version=2.7.5c STAR compilation time,server,dir=Sun Aug 16 18:27:20 EDT 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source ##### Command Line: STAR --runMode genomeGenerate --runThreadN 1 --sjdbGTFfile /var/lib/cwl/stg7c2ad2c7-9df1-475e-a853-37e4872e2a83/chr1-hg19_genes.gtf --genomeDir ./chr1 --genomeFastaFiles /var/lib/cwl/stgeb6769bb-e239-4e95-9983-d4bf5936dc37/chr1.fa --sjdbOverhang 99 ##### Initial USER parameters from Command Line: ###### All USER parameters from Command Line: runMode genomeGenerate ~RE-DEFINED runThreadN 1 ~RE-DEFINED sjdbGTFfile /var/lib/cwl/stg7c2ad2c7-9df1-475e-a853-37e4872e2a83/chr1-hg19_genes.gtf ~RE-DEFINED genomeDir ./chr1 ~RE-DEFINED genomeFastaFiles /var/lib/cwl/stgeb6769bb-e239-4e95-9983-d4bf5936dc37/chr1.fa ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runMode genomeGenerate runThreadN 1 genomeDir ./chr1 genomeFastaFiles /var/lib/cwl/stgeb6769bb-e239-4e95-9983-d4bf5936dc37/chr1.fa sjdbGTFfile /var/lib/cwl/stg7c2ad2c7-9df1-475e-a853-37e4872e2a83/chr1-hg19_genes.gtf sjdbOverhang 99 ------------------------------- ##### Final effective command line: STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ./chr1 --genomeFastaFiles /var/lib/cwl/stgeb6769bb-e239-4e95-9983-d4bf5936dc37/chr1.fa --sjdbGTFfile /var/lib/cwl/stg7c2ad2c7-9df1-475e-a853-37e4872e2a83/chr1-hg19_genes.gtf --sjdbOverhang 99 ---------------------------------------- Number of fastq files for each mate = 1 Finished loading and checking parameters --genomeDir directory created: ./chr1/ Jan 17 04:52:34 ... starting to generate Genome files /var/lib/cwl/stgeb6769bb-e239-4e95-9983-d4bf5936dc37/chr1.fa : chr # 0 "chr1" chrStart: 0 Chromosome sequence lengths: chr1 249250621 Genome sequence total length = 249250621 Genome size with padding = 249298944 Jan 17 04:52:38 ..... processing annotations GTF Processing pGe.sjdbGTFfile=/var/lib/cwl/stg7c2ad2c7-9df1-475e-a853-37e4872e2a83/chr1-hg19_genes.gtf, found: 3854 transcripts 37213 exons (non-collapsed) 20752 collapsed junctions Total junctions: 20752 Jan 17 04:52:38 ..... finished GTF processing !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=249250621, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 12 Estimated genome size with padding and SJs: total=genome+SJ=448298944 = 249298944 + 199000000 GstrandBit=32 Number of SA indices: 450561242 Jan 17 04:52:39 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 1; chunks size limit: 18300841144 bytes Jan 17 04:52:42 ... sorting Suffix Array chunks and saving them to disk... Writing 3604489936 bytes into ./chr1//SA_0 ; empty space on disk = 372217315328 bytes ... done Jan 17 04:57:25 ... loading chunks from disk, packing SA... Jan 17 04:57:30 ... finished generating suffix array Jan 17 04:57:30 ... generating Suffix Array index Jan 17 04:58:30 ... completed Suffix Array index Jan 17 04:58:30 Finished preparing junctions Jan 17 04:58:30 ..... inserting junctions into the genome indices Jan 17 04:58:50 Finished SA search: number of new junctions=20750, old junctions=0 Jan 17 04:58:51 Finished sorting SA indicesL nInd=8217000 Genome size with junctions=253428194 249298944 4129250 GstrandBit1=32 GstrandBit=32 Jan 17 04:58:57 Finished inserting junction indices Jan 17 04:59:04 Finished SAi Jan 17 04:59:04 ..... finished inserting junctions into genome Jan 17 04:59:04 ... writing Genome to disk ... Writing 253428194 bytes into ./chr1//Genome ; empty space on disk = 372216160256 bytes ... done SA size in bytes: 1892460252 Jan 17 04:59:04 ... writing Suffix Array to disk ... Writing 1892460252 bytes into ./chr1//SA ; empty space on disk = 371962728448 bytes ... done Jan 17 04:59:05 ... writing SAindex to disk Writing 8 bytes into ./chr1//SAindex ; empty space on disk = 370070233088 bytes ... done Writing 120 bytes into ./chr1//SAindex ; empty space on disk = 370070233088 bytes ... done Writing 1565873491 bytes into ./chr1//SAindex ; empty space on disk = 370070233088 bytes ... done Jan 17 04:59:06 ..... finished successfully DONE: Genome generation, EXITING