Tophat 2 Mapping left-kept-reads-seg1 to genome segment-juncs with Bowtie2 (1/4) error

[Masume Jomhori]

Dear members,

I'm looking to find a solution for my error in tophat2 running.
I'm using tophat2 to detect fusion junctions, I've run tophat for 3 different data, for new data I have constant error for mapping step.
By the way I've prepared my comment, system information, and run log for your consideration.
If I have your guidance, it would be a great help to me.
Thank you for your time.

I reinstalled Bowtie2, redownloading the reference genome but it didn't work.
My error is:
Mapping left-kept-reads-seg1 to genome segment-juncs with Bowtie2 (1/4)
[FAILED]

My Comment:
./tophat2 -p 8 --keep-fasta-order --fusion-search --library-type fr-unstranded -o '/media/razi/Razi/Jomhori/NGS/Files/GSE207248/SRR19907687/tophat2/' '/media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19' '/media/razi/Razi/Jomhori/NGS/Files/GSE207248/SRR19907687/trimming/SRR19907687_1.fastq' '/media/razi/Razi/Jomhori/NGS/Files/GSE207248/SRR19907687/trimming/SRR19907687_2.fastq'

System Information:
CPU: 8
RAM: 1G free
Memory: 52 G
Tophat version: 2.1.0
Bowtie version: 2.5.1

Run log:
./tophat -p 8 --keep-fasta-order --fusion-search --library-type fr-unstranded -o /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2/ /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ForwardPairs.fastq /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ReversePairs.fastq /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ForwardUnpairs.fastq /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ReverseUnpairs.fastq
#>prep_reads:
/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2// --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 --fusion-search --fusion-anchor-length 20 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p8 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --aux-outfile=/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//prep_reads.info --index-outfile=/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/%side%_kept_reads.bam.index --sam-header=/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam --outfile=/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/%side%_kept_reads.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ForwardPairs.fastq /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/trimming/SRR10804433_ReversePairs.fastq
#>map_start:
/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/bam2fastx --all /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads.bam|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads.mapped.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads.mapped.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4_unmapped.bam
/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/bam2fastx --all /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads.bam|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads.mapped.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads.mapped.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_unmapped.bam
#>map_segments:
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3_unmapped.bam
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19 -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4_unmapped.bam
#>find_juncs:
/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2// --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 --fusion-search --fusion-anchor-length 20 --fusion-min-dist 10000000 --fusion-read-mismatches 2 --fusion-multireads 2 --fusion-multipairs 2 -z gzip -p8 --inner-dist-mean 50 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/hg19_genome.bwt.samheader.sam --ium-reads /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3_unmapped.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4_unmapped.bam /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19.fa /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.juncs /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.insertions /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.deletions /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.fusions /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads.mapped.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg2.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg3.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg4.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads.mapped.bam /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg1.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg2.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg3.bam,/media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/right_kept_reads_seg4.bam
#>juncs_db:
/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/juncs_db 3 25 /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.juncs /dev/null /dev/null /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment.fusions /media/razi/Razi/Jomhori/NGS/Index_genome/Bowtie2_index/hg19.fa > /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment_juncs.fa
/media/razi/Razi/Jomhori/App/bowtie2/bowtie2-build /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment_juncs.fa /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment_juncs
#>map2juncs:
gzip -cd< /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.fq.z|/media/razi/Razi/Jomhori/App/bowtie2/bowtie2 -k 41 -N 1 -L 20 -p 8 --sam-no-hd -x /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment_juncs -|/media/razi/Razi/Jomhori/App/TopHat2/tophat-2.1.0.Linux_x86_64/fix_map_ordering --bowtie2-min-score 10 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.to_spliced.bam.index --sam-header /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/segment_juncs.bwt.samheader.sam - /media/razi/Razi/Jomhori/NGS/Files/GSE142731/SRR10804433/tophat2//tmp/left_kept_reads_seg1.to_spliced.bam