Question: Reporting output tracks FAILED in tophat
0
gravatar for yychangsd
2.1 years ago by
yychangsd30
yychangsd30 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
error tophat job local • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by yychangsd30
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Most likely the output location is not writable by the Galaxy process. There could be a lack of disk space, some network issue, or a permission conflict.

If the tool itself was running out of memory executing the job, there is usually a different type of error. However, if all else checks out, that is what to look at next.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
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