Question: Tophat in usegalaxy
0
gravatar for clizama
2.5 years ago by
clizama0
clizama0 wrote:

Hi,

I'm running galaxy in usegalaxy, I got these error. Previously I was running tophat in ami (amazon cloud), I got the same problem. I tried run the same files in different tophat version 2.014, 2.0.4, 2.0.5 and I got the same error, reading in different forum they told me is a bug that tophat has that could be fixed changing the number of threads (instead to use -p8 or 4 use -p1). The thinks is Im not running tophat in a command line i just using tophat from galaxy. Also, I found that the tophat 2.0.0 or 2.0.6 dosent have the problem, then I was wondering if someone know a galaxy (web server) that run some of this version of tophat just to try, or can help me with other solution.

Thanks Carlos

Fatal error: Tool execution failed

[2016-03-31 03:05:48] Beginning TopHat run (v2.0.14)

[2016-03-31 03:05:48] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-03-31 03:05:48] Checking for Bowtie index files (genome).. [2016-03-31 03:05:48] Checking for reference FASTA file [2016-03-31 03:05:48] Generating SAM header for /galaxy/data/mm10/bowtie2_index/mm10 [2016-03-31 03:06:15] Reading known junctions from GTF file [2016-03-31 03:06:19] Preparing reads left reads: min. length=100, max. length=100, 41508558 kept reads (53993 discarded) right reads: min. length=100, max. length=100, 41492545 kept reads (70006 discarded) [2016-03-31 03:34:53] Building transcriptome data files ./tophat_out/tmp/dataset_15019116 [2016-03-31 03:35:26] Building Bowtie index from dataset_15019116.fa [2016-03-31 03:41:06] Mapping left_kept_reads to transcriptome dataset_15019116 with Bowtie2 [2016-03-31 04:13:30] Mapping right_kept_reads to transcriptome dataset_15019116 with Bowtie2 [2016-03-31 04:47:59] Resuming TopHat pipeline with unmapped reads [2016-03-31 04:47:59] Mapping left_kept_reads.m2g_um to genome mm10 with Bowtie2 [2016-03-31 05:43:31] Mapping left_kept_reads.m2g_um_seg1 to genome mm10 with Bowtie2 (1/4) [2016-03-31 05:50:10] Mapping left_kept_reads.m2g_um_seg2 to genome mm10 with Bowtie2 (2/4) [2016-03-31 05:58:27] Mapping left_kept_reads.m2g_um_seg3 to genome mm10 with Bowtie2 (3/4) [2016-03-31 06:06:12] Mapping left_kept_reads.m2g_um_seg4 to genome mm10 with Bowtie2 (4/4) [2016-03-31 06:14:01] Mapping right_kept_reads.m2g_um to genome mm10 with Bowtie2 [2016-03-31 07:18:13] Mapping right_kept_reads.m2g_um_seg1 to genome mm10 with Bowtie2 (1/4) [2016-03-31 07:24:08] Mapping right_kept_reads.m2g_um_seg2 to genome mm10 with Bowtie2 (2/4) [2016-03-31 07:32:55] Mapping right_kept_reads.m2g_um_seg3 to genome mm10 with Bowtie2 (3/4) [2016-03-31 07:41:26] Mapping right_kept_reads.m2g_um_seg4 to genome mm10 with Bowtie2 (4/4) [2016-03-31 07:50:38] Searching for junctions via segment mapping [2016-03-31 08:08:53] Retrieving sequences for splices [2016-03-31 08:10:34] Indexing splices Building a SMALL index [2016-03-31 08:11:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) [2016-03-31 08:13:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) [2016-03-31 08:16:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) [2016-03-31 08:20:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) [2016-03-31 08:23:20] Joining segment hits [2016-03-31 08:29:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) [2016-03-31 08:31:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) [2016-03-31 08:34:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) [2016-03-31 08:38:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) [2016-03-31 08:42:19] Joining segment hits [2016-03-31 08:48:18] Reporting output tracks [FAILED] Error running /galaxy-repl/main/deps/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/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 -p6 --inner-dist-mean 200 --inner-dist-std-dev 20 --gtf-annotations /galaxy-repl/main/files/015/019/dataset_15019116.dat --gtf-juncs ./tophat_out/tmp/dataset_15019116.juncs --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header ./tophat_out/tmp/mm10_genome.bwt.samheader.sam --report-mixed-alignments --samtools=/galaxy-repl/main/deps/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/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 /galaxy/data/mm10/bowtie2_index/mm10.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 212063 junctions

rna-seq • 1.0k views
ADD COMMENTlink written 2.5 years ago by clizama0

Hello, Can you share the link to the bug fix/workaround? Thanks, Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

Hi jen,

http://seqanswers.com/forums/showthread.php?t=24205

https://groups.google.com/forum/#!topic/tuxedo-tools-users/0pcEVAOCBaw

https://www.biostars.org/p/101767/

I have these three links in the first one they explain is a numbers of threads problem in the second one the version of tophat.

Thanks Carlos

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by clizama0

https://www.biostars.org/p/102197/

ADD REPLYlink written 2.5 years ago by clizama0

Hi Jen,

Did you find a way to fix the problem?

Thanks Carlos

ADD REPLYlink written 2.5 years ago by clizama0
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