tophat error help

Question

[clizama]

I was running tophat using galaxy in amazon cloud and I git this error, someone can help me to fix it.

[2016-03-24 07:39:10] Checking for Bowtie Bowtie version: 2.2.3.0 
[2016-03-24 07:39:10] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. 
[2016-03-24 07:39:10] Checking for reference FASTA file 
[2016-03-24 07:39:10] Generating SAM header for /data/refs/mm10/genome.fa 
[2016-03-24 07:39:34] Reading known junctions from GTF file 
[2016-03-24 07:39:36] Preparing reads left reads: min. length=20, max. length=100, 41391601 kept reads (96792 discarded) right reads: min. length=20, max. length=100, 41365359 kept reads (123034 discarded) 
[2016-03-24 08:06:07] Building transcriptome data files ./tophat_out/tmp/genes 
[2016-03-24 08:06:31] Building Bowtie index from genes.fa 
[2016-03-24 08:09:56] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-03-24 08:44:53] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-03-24 09:19:32] Resuming TopHat pipeline with unmapped reads 
[2016-03-24 09:19:32] Mapping left_kept_reads.m2g_um to genome genome.fa with Bowtie2 
[2016-03-24 10:18:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome.fa with Bowtie2 (1/4) 
[2016-03-24 10:25:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome.fa with Bowtie2 (2/4) 
[2016-03-24 10:31:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome.fa with Bowtie2 (3/4) 
[2016-03-24 10:37:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome.fa with Bowtie2 (4/4) 
[2016-03-24 10:43:53] Mapping right_kept_reads.m2g_um to genome genome.fa with Bowtie2 
[2016-03-24 11:45:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome.fa with Bowtie2 (1/4) 
[2016-03-24 11:52:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome.fa with Bowtie2 (2/4) 
[2016-03-24 12:00:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome.fa with Bowtie2 (3/4) 
[2016-03-24 12:07:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome.fa with Bowtie2 (4/4) 
[2016-03-24 12:13:35] Searching for junctions via segment mapping 
[2016-03-24 12:26:03] Retrieving sequences for splices 
[2016-03-24 12:27:17] Indexing splices Building a SMALL index 
[2016-03-24 12:27:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) 
[2016-03-24 12:29:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) 
[2016-03-24 12:31:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) 
[2016-03-24 12:34:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) 
[2016-03-24 12:36:54] Joining segment hits 
[2016-03-24 12:42:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) 
[2016-03-24 12:44:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) 
[2016-03-24 12:47:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) 
[2016-03-24 12:50:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) 
[2016-03-24 12:53:30] Joining segment hits 
[2016-03-24 12:59:36] Reporting output tracks [FAILED] Error running /software/tophat/2.0.13/x86_64-linux-ubuntu14.04/bin/tophat_reports \
--min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ \
--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 1000 --max-insertion-length 3 --max-deletion-length 3 \
-z gzip -p4 --inner-dist-mean 200 --inner-dist-std-dev 20 --gtf-annotations /data/refs/mm10/genes.gtf --gtf-juncs \
./tophat_out/tmp/genes.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded \
--sam-header ./tophat_out/tmp/genome.fa_genome.bwt.samheader.sam --report-mixed-alignments \
--samtools=/software/tophat/2.0.13/x86_64-linux-ubuntu14.04/bin/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 \
/data/refs/mm10/genome.fa.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out \
./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.m2g.bam,./tophat_out/tmp/left_kept_reads.m2g_um.mapped.bam,./tophat_out/tmp/left_kept_reads.m2g_um.candidates \
./tophat_out/tmp/left_kept_reads.bam ./tophat_out/tmp/right_kept_reads.m2g.bam,./tophat_out/tmp/right_kept_reads.m2g_um.mapped.bam,./tophat_out/tmp/right_kept_reads.m2g_um.candidates \
./tophat_out/tmp/right_kept_reads.bam Loaded 209433 junctions

Thanks carlos

[gangireddy]

See this link and similar posts below

[clizama]

Yeah I'm working in try to change the number of threads, my problem is Im runing tophat in galaxy and I couldnt find the option to change the number of threads from 8 to 1.

[Devon Ryan]

If you're running this in Galaxy then this isn't an option you can change. You're going to need to contact the administrator of the Galaxy instance you're using for further help with that.

[Ram]

Code reformatted for readability.