##### Final parameters after user input--------------------------------: versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 4 runDirPerm User_RWX runRNGseed 777 genomeDir /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1 genomeLoad NoSharedMemory genomeFastaFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 readFilesIn /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ ATTACTCG-GGCTCTGA_L002_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB3 7_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/J B37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_downlo ad/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_down load/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_do wnload/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_ download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq readFilesCommand - readMatesLengthsIn NotEqual readMapNumber 18446744073709551615 readNameSeparator / inputBAMfile - bamRemoveDuplicatesType - bamRemoveDuplicatesMate2basesN 0 limitGenomeGenerateRAM 31000000000 limitIObufferSize 150000000 limitOutSAMoneReadBytes 100000 limitOutSJcollapsed 1000000 limitOutSJoneRead 1000 limitBAMsortRAM 0 limitSjdbInsertNsj 1000000 outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA outTmpDir - outTmpKeep None outStd Log outReadsUnmapped None outQSconversionAdd 0 outMultimapperOrder Old_2.4 outSAMtype BAM SortedByCoordinate 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 1 outFilterMultimapScoreRange 1 outFilterScoreMin 0 outFilterScoreMinOverLread 0 outFilterMatchNmin 0 outFilterMatchNminOverLread 0 outFilterMismatchNmax 2 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 chimJunctionOverhangMin 20 chimOutType SeparateSAMold chimFilter banGenomicN chimSegmentReadGapMax 0 sjdbFileChrStartEnd - sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/STARindex_MacaM/macam_annot/MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 100 sjdbScore 2 sjdbInsertSave Basic quantMode GeneCounts quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None ---------------------------------------- Input read files for mate 1, from input string /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGT I_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_V GTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627 _VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 666790221 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656995965 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656034791 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 649712788 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 659414483 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 660493219 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 661592981 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq readsCommandsFile: exec > "/hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA_STARtmp/tmp.fifo.read1" echo FILE 0 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R1_001.fastq" echo FILE 1 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R1_001.fastq" echo FILE 2 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R1_001.fastq" echo FILE 3 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R1_001.fastq" echo FILE 4 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R1_001.fastq" echo FILE 5 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R1_001.fastq" echo FILE 6 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R1_001.fastq" Input read files for mate 2, from input string /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGT I_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_V GTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627 _VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq,/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 666790221 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656995965 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 656034791 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 649712788 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 659414483 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 660493219 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq -rwxrwxrwx+ 1 leerkesm bcbb 661592981 Sep 11 2014 /hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq readsCommandsFile: exec > "/hpcdata/lmm/lmm_data/muddjc/STARindex_Mmul/JB37_ATTACTCG-GGCTCTGA/JB37_ATTACTCG-GGCTCTGA_STARtmp/tmp.fifo.read2" echo FILE 0 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L001_R2_001.fastq" echo FILE 1 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L002_R2_001.fastq" echo FILE 2 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L003_R2_001.fastq" echo FILE 3 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L004_R2_001.fastq" echo FILE 4 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L005_R2_001.fastq" echo FILE 5 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L006_R2_001.fastq" echo FILE 6 cat "/hpcdata/bcbb/leerkesm/AGM/WGET_FTP_48/FTP_627_VGTI_download/JB37_ATTACTCG-GGCTCTGA_L007_R2_001.fastq" WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting Finished loading and checking parameters Reading genome generation parameters: versionGenome 20201 ~RE-DEFINED genomeFastaFiles /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.fna ~RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED genomeChrBinNbits 0 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile /hpcdata/lmm/lmm_data/muddjc/Mmul_8.0.1/GCF_000772875.2_Mmul_8.0.1_genomic.gff ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscriptParent ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED Genome version is compatible with current STAR version Number of real (reference) chromosomes= 284728 1 NC_027893.1 225584828 0 2 NC_027894.1 204787373 225584830 3 NC_027895.1 185818997 430372205 4 NC_027896.1 172585720 616191204 5 NC_027897.1 190429646 788776926 6 NC_027898.1 180051392 979206574 7 NC_027899.1 169600520 1159257968 8 NC_027900.1 144306982 1328858490 9 NC_027901.1 129882849 1473165474 10 NC_027902.1 92844088 1603048325 11 NC_027903.1 133663169 1695892415 12 NC_027904.1 125506784 1829555586 13 NC_027905.1 108979918 1955062372 14 NC_027906.1 127894412 2064042292 15 NC_027907.1 111343173 2191936706 16 NC_027908.1 77216781 2303279881 17 NC_027909.1 95684472 2380496664 18 NC_027910.1 70235451 2476181138 19 NC_027911.1 53671032 2546416591 20 NC_027912.1 74971481 2600087625 21 NC_027913.1 149150640 2675059108 22 NC_027914.1 11753682 2824209750 23 NW_014806053.1 1653 2835963434 24 NW_014806054.1 997 2835965089 25 NW_014806055.1 843 2835966088 26 NW_014806056.1 783 2835966933 27 NW_014806057.1 655 2835967718 28 NW_014806058.1 712 2835968375 29 NW_014806059.1 994 2835969089 30 NW_014806060.1 7901 2835970085 31 NW_014806061.1 822 2835977988 ################################....etc...################################## chrX blastn exon 148854682 148854749 . + . gene_id "6845"; transcript_id "VAMP7_transcript_01"; gene_name "VAMP7"; gene_description "vesicle-associated membrane protein 7"; WARNING: while processing sjdbGTFfile=/hpcdata/lmm/lmm_data/muddjc/STARindex_MacaM/macam_annot/MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf: chromosome 'chrX' not found in Genome fasta files for line: chrX blastn exon 148873137 148873229 . + . gene_id "6845"; transcript_id "VAMP7_transcript_01"; gene_name "VAMP7"; gene_description "vesicle-associated membrane protein 7"; WARNING: while processing sjdbGTFfile=/hpcdata/lmm/lmm_data/muddjc/STARindex_MacaM/macam_annot/MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf: chromosome 'chrX' not found in Genome fasta files for line: chrX blastn exon 148875605 148877459 . + . gene_id "6845"; transcript_id "VAMP7_transcript_01"; gene_name "VAMP7"; gene_description "vesicle-associated membrane protein 7"; Fatal INPUT FILE error, no valid exon lines in the GTF file: /hpcdata/lmm/lmm_data/muddjc/STARindex_MacaM/macam_annot/MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf Solution: check the formatting of the GTF file. Most likely cause is the difference in chromosome naming between GTF and FASTA file. Nov 10 10:42:45 ...... FATAL ERROR, exiting