Question: Reporting output tracks FAILED in tophat
0
yychangsd • 30 wrote:
I got an error from topcoat.
Any suggestions would be appreciated~~
Thanks~
[2016-09-19 16:33:04] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2016-09-19 16:33:04] Checking for Bowtie
Bowtie version: 2.1.0.0
[2016-09-19 16:33:04] Checking for Samtools
Samtools version: 0.1.19.0
[2016-09-19 16:33:04] Checking for Bowtie index files (genome)..
[2016-09-19 16:33:04] Checking for reference FASTA file
[2016-09-19 16:33:04] Generating SAM header for /home/oasis/data/NGS-ann-project/refs/ensembl-genomes/c.elegan
[2016-09-19 16:33:05] Reading known junctions from GTF file
[2016-09-19 16:33:10] Preparing reads
left reads: min. length=75, max. length=75, 2500000 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 2500000 kept reads (0 discarded)
[2016-09-19 16:33:40] Building transcriptome data files qc-tophat-cufflink-pe/tophat/tmp/c.elegan
[2016-09-19 16:33:46] Building Bowtie index from c.elegan.fa
[2016-09-19 16:37:39] Mapping left_kept_reads to transcriptome c.elegan with Bowtie2
[2016-09-19 16:38:08] Mapping right_kept_reads to transcriptome c.elegan with Bowtie2
[2016-09-19 16:38:37] Resuming TopHat pipeline with unmapped reads
[2016-09-19 16:38:37] Mapping left_kept_reads.m2g_um to genome c.elegan with Bowtie2
[2016-09-19 16:41:24] Mapping left_kept_reads.m2g_um_seg1 to genome c.elegan with Bowtie2 (1/3)
[2016-09-19 16:42:09] Mapping left_kept_reads.m2g_um_seg2 to genome c.elegan with Bowtie2 (2/3)
[2016-09-19 16:42:55] Mapping left_kept_reads.m2g_um_seg3 to genome c.elegan with Bowtie2 (3/3)
[2016-09-19 16:43:40] Mapping right_kept_reads.m2g_um to genome c.elegan with Bowtie2
[2016-09-19 16:46:18] Mapping right_kept_reads.m2g_um_seg1 to genome c.elegan with Bowtie2 (1/3)
[2016-09-19 16:46:48] Mapping right_kept_reads.m2g_um_seg2 to genome c.elegan with Bowtie2 (2/3)
[2016-09-19 16:47:18] Mapping right_kept_reads.m2g_um_seg3 to genome c.elegan with Bowtie2 (3/3)
[2016-09-19 16:47:47] Searching for junctions via segment mapping
[2016-09-19 16:48:10] Retrieving sequences for splices
[2016-09-19 16:48:13] Indexing splices
[2016-09-19 16:48:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2016-09-19 16:48:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2016-09-19 16:48:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2016-09-19 16:49:08] Joining segment hits
[2016-09-19 16:49:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2016-09-19 16:49:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2016-09-19 16:49:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2016-09-19 16:50:06] Joining segment hits
[2016-09-19 16:50:18] Reporting output tracks
[FAILED]
Error running /home/oasis/data/NGS-ann-project/apps/tophat-2.0.12.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 qc-tophat-cufflink-pe/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 -p4 --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations /home/oasis/data/NGS-ann-project/refs/ensembl-genomes/c.elegan.gtf --gtf-juncs qc-tophat-cufflink-pe/tophat/tmp/c.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header qc-tophat-cufflink-pe/tophat/tmp/c.elegan_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/home/oasis/data/NGS-ann-project/apps/bin/samtools --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 /home/oasis/data/NGS-ann-project/refs/ensembl-genomes/c.elegan.fa qc-tophat-cufflink-pe/tophat/junctions.bed qc-tophat-cufflink-pe/tophat/insertions.bed qc-tophat-cufflink-pe/tophat/deletions.bed qc-tophat-cufflink-pe/tophat/fusions.out qc-tophat-cufflink-pe/tophat/tmp/accepted_hits qc-tophat-cufflink-pe/tophat/tmp/left_kept_reads.bam
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modified 2.2 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.2 years ago by
yychangsd • 30
