Hello All I am running tophat v2.1.1 on human sample pairend reads (6.0 gb data) after running for 5-6 hour i am getting this error :-
Error running /home/installations/tophat-2.1.1.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir Sample_89_tophat/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p8 --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations ./ref_gtf_files/hg19.gtf --gtf-juncs Sample_89_tophat/tmp/hg19.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header Sample_89_tophat/tmp/hg19_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/home//installations/tophat-2.1.1.Linux_x86_64/samtools_0.1.18 --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 ./ref_gtf_files/hg19.fa Sample_89_tophat/junctions.bed Sample_89_tophat/insertions.bed Sample_89_tophat/deletions.bed Sample_89_tophat/fusions.out Sample_89_tophat/tmp/accepted_hits Sample_89_tophat/tmp/left_kept_reads.m2g.bam,Sample_89_tophat/tmp/left_kept_reads.m2g_um.mapped.bam,Sample_89_tophat/tmp/left_kept_reads.m2g_um.candidates Sample_89_tophat/tmp/left_kept_reads.bam Sample_89_tophat/tmp/right_kept_reads.m2g.bam,Sample_89_tophat/tmp/right_kept_reads.m2g_um.mapped.bam,Sample_89_tophat/tmp/right_kept_reads.m2g_um.candidates Sample_89_tophat/tmp/right_kept_reads.bam
Error: ReadStream::getRead() called with out-of-order id#!
