STAR version=STAR_2.5.3a STAR compilation time,server,dir=Fri Mar 17 11:35:46 EDT 2017 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source ##### DEFAULT parameters: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn Read1 Read2 readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype SAM outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped None outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline - outSAMheaderHD - outSAMheaderPG - outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None outSAMmultNmax 18446744073709551615 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1 outSJfilterCountTotalMin 3 1 1 1 outSJfilterOverhangMin 30 12 12 12 outSJfilterDistToOtherSJmin 10 0 5 10 outSJfilterIntronMaxVsReadN 50000 100000 200000 outWigType None outWigStrand Stranded outWigReferencesPrefix - outWigNorm RPM outFilterType Normal outFilterMultimapNmax 10 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 1 outFilterIntronMotifs None clip5pNbases 0 clip3pNbases 0 clip3pAfterAdapterNbases 0 clip3pAdapterSeq - clip3pAdapterMMp 0.1 winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 21 alignIntronMax 0 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSJstitchMismatchNmax 0 -1 0 0 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile - sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ##### Command Line: STAR --genomeDir /data/share/htp/zUMIs_paper/tiny_testdata/reference/hg38_chr22/ --runThreadN 8 --readFilesCommand zcat --sjdbGTFfile /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf --outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. --outSAMtype BAM Unsorted --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --sjdbOverhang 49 --twopassMode Basic --readFilesIn /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz ##### Initial USER parameters from Command Line: outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. ###### All USER parameters from Command Line: genomeDir /data/share/htp/zUMIs_paper/tiny_testdata/reference/hg38_chr22/ ~RE-DEFINED runThreadN 8 ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED sjdbGTFfile /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf ~RE-DEFINED outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED outSAMmultNmax 1 ~RE-DEFINED outFilterMultimapNmax 50 ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED sjdbOverhang 49 ~RE-DEFINED twopassMode Basic ~RE-DEFINED readFilesIn /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 8 genomeDir /data/share/htp/zUMIs_paper/tiny_testdata/reference/hg38_chr22/ readFilesIn /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz readFilesCommand zcat outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. outSAMtype BAM Unsorted outSAMunmapped Within outSAMmultNmax 1 outFilterMultimapNmax 50 sjdbGTFfile /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf sjdbOverhang 49 twopassMode Basic ------------------------------- ##### Final effective command line: STAR --runThreadN 8 --genomeDir /data/share/htp/zUMIs_paper/tiny_testdata/reference/hg38_chr22/ --readFilesIn /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz --readFilesCommand zcat --outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. --outSAMtype BAM Unsorted --outSAMunmapped Within --outSAMmultNmax 1 --outFilterMultimapNmax 50 --sjdbGTFfile /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf --sjdbOverhang 49 --twopassMode Basic ##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 8 runDirPerm User_RWX runRNGseed 777 genomeDir /data/share/htp/zUMIs_paper/tiny_testdata/reference/hg38_chr22/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 readFilesIn /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz readFilesCommand zcat readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test. outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM Unsorted outSAMmode Full outSAMstrandField None outSAMattributes Standard outSAMunmapped Within outSAMorder Paired outSAMprimaryFlag OneBestScore outSAMreadID Standard outSAMmapqUnique 255 outSAMflagOR 0 outSAMflagAND 65535 outSAMattrRGline - outSAMheaderHD - outSAMheaderPG - outSAMheaderCommentFile - outBAMcompression 1 outBAMsortingThreadN 0 outSAMfilter None outSAMmultNmax 1 outSAMattrIHstart 1 outSJfilterReads All outSJfilterCountUniqueMin 3 1 1 1 outSJfilterCountTotalMin 3 1 1 1 outSJfilterOverhangMin 30 12 12 12 outSJfilterDistToOtherSJmin 10 0 5 10 outSJfilterIntronMaxVsReadN 50000 100000 200000 outWigType None outWigStrand Stranded outWigReferencesPrefix - outWigNorm RPM outFilterType Normal outFilterMultimapNmax 50 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0.66 outFilterMatchNmin 0 outFilterMatchNminOverLread 0.66 outFilterMismatchNmax 10 outFilterMismatchNoverLmax 0.3 outFilterMismatchNoverReadLmax 1 outFilterIntronMotifs None clip5pNbases 0 clip3pNbases 0 clip3pAfterAdapterNbases 0 clip3pAdapterSeq - clip3pAdapterMMp 0.1 winBinNbits 16 winAnchorDistNbins 9 winFlankNbins 4 winAnchorMultimapNmax 50 winReadCoverageRelativeMin 0.5 winReadCoverageBasesMin 0 scoreGap 0 scoreGapNoncan -8 scoreGapGCAG -4 scoreGapATAC -8 scoreStitchSJshift 1 scoreGenomicLengthLog2scale -0.25 scoreDelBase -2 scoreDelOpen -2 scoreInsOpen -2 scoreInsBase -2 seedSearchLmax 0 seedSearchStartLmax 50 seedSearchStartLmaxOverLread 1 seedPerReadNmax 1000 seedPerWindowNmax 50 seedNoneLociPerWindow 10 seedMultimapNmax 10000 alignIntronMin 21 alignIntronMax 0 alignMatesGapMax 0 alignTranscriptsPerReadNmax 10000 alignSJoverhangMin 5 alignSJDBoverhangMin 3 alignSJstitchMismatchNmax 0 -1 0 0 alignSplicedMateMapLmin 0 alignSplicedMateMapLminOverLmate 0.66 alignWindowsPerReadNmax 10000 alignTranscriptsPerWindowNmax 100 alignEndsType Local alignSoftClipAtReferenceEnds Yes alignEndsProtrude 0 ConcordantPair chimSegmentMin 0 chimScoreMin 0 chimScoreDropMax 20 chimScoreSeparation 10 chimScoreJunctionNonGTAG -1 chimMainSegmentMultNmax 10 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 49 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz -rw-r--r-- 1 ziegenhain ngs 40267821 Jul 20 00:44 /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz readsCommandsFile: exec > "/data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz" Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles Homo_sapiens.GRCh38.dna.chromosome.22.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 0 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile - ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 50855936 323068164 ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 1 1 chr22 50818468 0 Started loading the genome: Thu Jul 20 00:44:19 2017 Genome: size given as a parameter = 50855936 SA: size given as a parameter = 323068164 /SAindex: size given as a parameter = 1 Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 nGenome=50855936; nSAbyte=323068164 GstrandBit=32 SA number of indices=78319554 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 50855936 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 50855936 bytes SA file size: 323068164 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 323068164 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Thu Jul 20 00:44:21 2017 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Jul 20 00:44:21 ..... processing annotations GTF WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 117447 117524 . + . gene_id ENSG00000276330; gene_version 1; transcript_id ENST00000615878; transcript_version 1; exon_number 1; gene_name AL353644.7; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.7-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003734725; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 121581 121672 . + . gene_id ENSG00000274411; gene_version 1; transcript_id ENST00000610864; transcript_version 1; exon_number 1; gene_name hsa-mir-6724-1; gene_source ensembl; gene_biotype miRNA; transcript_name hsa-mir-6724-1.1-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003713658; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 122136 122225 . + . gene_id ENSG00000273739; gene_version 1; transcript_id ENST00000618675; transcript_version 1; exon_number 1; gene_name pRNA; gene_source ensembl; gene_biotype misc_RNA; transcript_name pRNA.1-201; transcript_source ensembl; transcript_biotype misc_RNA; exon_id ENSE00003734247; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 124297 124410 . + . gene_id ENSG00000275684; gene_version 1; transcript_id ENST00000610594; transcript_version 1; exon_number 1; gene_name AL353644.5; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.5-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003738251; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 124758 124937 . + . gene_id ENSG00000276112; gene_version 1; transcript_id ENST00000611782; transcript_version 1; exon_number 1; gene_name AL353644.6; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.6-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003732258; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 125129 125189 . + . gene_id ENSG00000277928; gene_version 1; transcript_id ENST00000611919; transcript_version 1; exon_number 1; gene_name hsa-mir-3687-1; gene_source ensembl; gene_biotype miRNA; transcript_name hsa-mir-3687-1.2-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003743707; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 128877 129029 . + . gene_id ENSG00000276700; gene_version 1; transcript_id ENST00000616292; transcript_version 1; exon_number 1; gene_name RNA5-8S5; gene_source ensembl; gene_biotype rRNA; transcript_name RNA5-8S5-205; transcript_source ensembl; transcript_biotype rRNA; exon_id ENSE00003725298; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 131007 131098 . + . gene_id ENSG00000277765; gene_version 1; transcript_id ENST00000611802; transcript_version 1; exon_number 1; gene_name AL353644.11; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.11-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003711757; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 134291 134339 . + . gene_id ENSG00000276402; gene_version 1; transcript_id ENST00000617577; transcript_version 1; exon_number 1; gene_name AL353644.8; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.8-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003731746; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 135060 135116 . + . gene_id ENSG00000277048; gene_version 1; transcript_id ENST00000611934; transcript_version 1; exon_number 1; gene_name AL353644.10; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.10-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003735886; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 166663 166754 . + . gene_id ENSG00000274745; gene_version 1; transcript_id ENST00000619285; transcript_version 1; exon_number 1; gene_name AL353644.2; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.2-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003746428; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 167218 167307 . + . gene_id ENSG00000276312; gene_version 1; transcript_id ENST00000615130; transcript_version 1; exon_number 1; gene_name pRNA; gene_source ensembl; gene_biotype misc_RNA; transcript_name pRNA.8-201; transcript_source ensembl; transcript_biotype misc_RNA; exon_id ENSE00003727949; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 169383 169496 . + . gene_id ENSG00000276936; gene_version 1; transcript_id ENST00000616001; transcript_version 1; exon_number 1; gene_name AL353644.9; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.9-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003729482; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 169844 170023 . + . gene_id ENSG00000275104; gene_version 1; transcript_id ENST00000615249; transcript_version 1; exon_number 1; gene_name AL353644.4; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.4-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003724824; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 170215 170275 . + . gene_id ENSG00000274016; gene_version 1; transcript_id ENST00000619716; transcript_version 1; exon_number 1; gene_name hsa-mir-3687-1; gene_source ensembl; gene_biotype miRNA; transcript_name hsa-mir-3687-1.1-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003735874; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 173956 174108 . + . gene_id ENSG00000275757; gene_version 1; transcript_id ENST00000618998; transcript_version 1; exon_number 1; gene_name RNA5-8S5; gene_source ensembl; gene_biotype rRNA; transcript_name RNA5-8S5-204; transcript_source ensembl; transcript_biotype rRNA; exon_id ENSE00003724737; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 176086 176177 . + . gene_id ENSG00000274804; gene_version 1; transcript_id ENST00000612700; transcript_version 1; exon_number 1; gene_name AL353644.3; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.3-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003729505; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270733v1_random' not found in Genome fasta files for line: chr22_KI270733v1_random ensembl exon 179370 179418 . + . gene_id ENSG00000274224; gene_version 1; transcript_id ENST00000621427; transcript_version 1; exon_number 1; gene_name AL353644.1; gene_source ensembl; gene_biotype miRNA; transcript_name AL353644.1-201; transcript_source ensembl; transcript_biotype miRNA; exon_id ENSE00003718377; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 59711 60178 . + . gene_id ENSG00000278573; gene_version 1; transcript_id ENST00000615362; transcript_version 1; exon_number 1; gene_name AC007325.3; gene_source ensembl; gene_biotype pseudogene; transcript_name AC007325.3-201; transcript_source ensembl; transcript_biotype pseudogene; exon_id ENSE00003744323; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 60182 60316 . + . gene_id ENSG00000278573; gene_version 1; transcript_id ENST00000615362; transcript_version 1; exon_number 2; gene_name AC007325.3; gene_source ensembl; gene_biotype pseudogene; transcript_name AC007325.3-201; transcript_source ensembl; transcript_biotype pseudogene; exon_id ENSE00003747300; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 72411 74814 . + . gene_id ENSG00000276017; gene_version 1; transcript_id ENST00000617983; transcript_version 1; exon_number 1; gene_name AC007325.1; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.1-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003721512; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 131494 131755 . + . gene_id ENSG00000278817; gene_version 1; transcript_id ENST00000613204; transcript_version 1; exon_number 1; gene_name AC007325.4; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.4-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003729133; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 131836 131996 . + . gene_id ENSG00000278817; gene_version 1; transcript_id ENST00000613204; transcript_version 1; exon_number 2; gene_name AC007325.4; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.4-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003729010; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 135443 135543 . + . gene_id ENSG00000278817; gene_version 1; transcript_id ENST00000613204; transcript_version 1; exon_number 3; gene_name AC007325.4; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.4-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003716987; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 136159 136299 . + . gene_id ENSG00000278817; gene_version 1; transcript_id ENST00000613204; transcript_version 1; exon_number 4; gene_name AC007325.4; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.4-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003730904; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 136845 137392 . + . gene_id ENSG00000278817; gene_version 1; transcript_id ENST00000613204; transcript_version 1; exon_number 5; gene_name AC007325.4; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.4-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003712507; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 161689 161852 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 1; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003746084; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 161314 161626 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 2; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003719550; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 156289 156497 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 3; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003723757; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 150987 151021 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 4; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003731891; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 150350 150499 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 5; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003724613; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 148414 148478 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 6; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003732418; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 148116 148232 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 7; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003733960; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 147624 147703 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 8; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003727207; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 146640 146721 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 9; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003728972; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 145004 145096 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 10; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003733844; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 144749 144895 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 11; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003752738; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 143614 143789 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 12; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003720006; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 142194 142292 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 13; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003719283; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 138743 138831 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 14; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003751415; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 138082 138667 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000621424; transcript_version 4; exon_number 15; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003753010; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 161689 161750 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 1; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003735197; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 156289 156497 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 2; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003737280; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 150987 151021 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 3; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003731891; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 150350 150499 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 4; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003724613; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 148414 148478 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 5; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003732418; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 148116 148232 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 6; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003733960; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 147624 147703 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 7; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003727207; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 146640 146721 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 8; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003728972; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 145004 145096 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 9; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003733844; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 144749 144895 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 10; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003752738; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 143614 143789 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 11; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003720006; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 142194 142292 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 12; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003719283; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 138743 138831 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 13; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003751415; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270734v1_random' not found in Genome fasta files for line: chr22_KI270734v1_random ensembl exon 138082 138667 . - . gene_id ENSG00000277196; gene_version 4; transcript_id ENST00000615165; transcript_version 1; exon_number 14; gene_name AC007325.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC007325.2-202; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003753010; exon_version 1; tag basic; transcript_support_level 1; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270731v1_random' not found in Genome fasta files for line: chr22_KI270731v1_random ensembl exon 10598 13001 . - . gene_id ENSG00000278633; gene_version 1; transcript_id ENST00000619792; transcript_version 1; exon_number 1; gene_name AC023491.2; gene_source ensembl; gene_biotype protein_coding; transcript_name AC023491.2-201; transcript_source ensembl; transcript_biotype protein_coding; exon_id ENSE00003722305; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270731v1_random' not found in Genome fasta files for line: chr22_KI270731v1_random ensembl exon 26671 27138 . - . gene_id ENSG00000278066; gene_version 1; transcript_id ENST00000620795; transcript_version 1; exon_number 1; gene_name AC023491.1; gene_source ensembl; gene_biotype pseudogene; transcript_name AC023491.1-201; transcript_source ensembl; transcript_biotype pseudogene; exon_id ENSE00003752618; exon_version 1; tag basic; transcript_support_level NA; WARNING: while processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: chromosome 'chr22_KI270731v1_random' not found in Genome fasta files for line: chr22_KI270731v1_random ensembl exon 26533 26667 . - . gene_id ENSG00000278066; gene_version 1; transcript_id ENST00000620795; transcript_version 1; exon_number 2; gene_name AC023491.1; gene_source ensembl; gene_biotype pseudogene; transcript_name AC023491.1-201; transcript_source ensembl; transcript_biotype pseudogene; exon_id ENSE00003754098; exon_version 1; tag basic; transcript_support_level NA; Processing sjdbGTFfile=/data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf, found: 4511 transcripts 26073 exons (non-collapsed) 7638 collapsed junctions Jul 20 00:44:22 ..... finished GTF processing Jul 20 00:44:22 Loaded database junctions from the GTF file: /data/share/htp/zUMIs_paper/tiny_testdata/reference/GRCh38.84.chr22.gtf: 7638 total junctions Jul 20 00:44:22 Finished preparing junctions Jul 20 00:44:22 ..... inserting junctions into the genome indices Jul 20 00:44:23 Finished SA search: number of new junctions=7634, old junctions=0 Jul 20 00:44:23 Finished sorting SA indicesL nInd=1496264 Jul 20 00:44:25 Finished inserting junction indices Jul 20 00:44:39 Finished SAi Jul 20 00:44:39 ..... finished inserting junctions into genome Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Starting to map file # 0 mate 1: /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz Thread #4 end of input stream, nextChar=-1 Completed: thread #6 Completed: thread #0 Completed: thread #7 Completed: thread #4 Completed: thread #5 Completed: thread #2 Completed: thread #3 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Jul 20 00:46:53 Loaded database junctions from the 1st pass file: /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test._STARpass1//SJ.out.tab: 15012 total junctions Jul 20 00:46:53 Finished preparing junctions Jul 20 00:46:53 ..... inserting junctions into the genome indices Jul 20 00:46:54 Finished SA search: number of new junctions=7088, old junctions=7634 Jul 20 00:46:54 Finished sorting SA indicesL nInd=1389248 Jul 20 00:46:56 Finished inserting junction indices Jul 20 00:47:10 Finished SAi Jul 20 00:47:10 ..... finished inserting junctions into genome Input read files for mate 1, from input string /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz -rw-r--r-- 1 ziegenhain ngs 40267821 Jul 20 00:44 /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz readsCommandsFile: exec > "/data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test._STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz" Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Starting to map file # 0 mate 1: /data/share/htp/zUMIs_paper/tiny_testdata/ExampleData//test.cdnaread.filtered.fastq.gz Thread #0 end of input stream, nextChar=-1 Completed: thread #7 Completed: thread #5 Completed: thread #6 Completed: thread #0 Completed: thread #1 Joined thread # 1 Completed: thread #3 Completed: thread #2 Joined thread # 2 Joined thread # 3 Completed: thread #4 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 ALL DONE!