I hope someone can advise or assist me with a tophat error. terminal output is below. error is:
Report generation failed with err = -11
I'm just starting to work with tophat. Ran it once on a single set of paired-end seqs and it finished OK. But then I got greedy and gave it 28 different sets of reads. Note that because of multiplexing samples this was not totally insane (I think) -- only 2 x 5.7e7 reads.
My current analysis goal is to use these data to generate a Cufflinks annotation for a novel butterfly genome. samples are from different individuals and tissues.
working on a linux cluster with 3TB diskspace and should have plenty of RAM/processors.
Current plan is to rerun with more modest allowance of datasets to see what happens, and/or on offending dataset (if I can fish out that detail from logs -- suggestions on that front welcome as well...)
Many Thanks, Jamie
_______________________________________
nice tophat -r 0 -i 20 -I 30000 -p 6 -g 20 --closure-search --min-closure-exon 20 --min-closure-intron 20 --min-coverage-intron 20 --min-segment-intron 20 --max-segment-intron 30000 indexes/melpomene
[Wed Feb 9 16:58:56 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Wed Feb 9 16:58:56 2011] Preparing output location edinburg_tophat_out/
[Wed Feb 9 16:58:56 2011] Checking for Bowtie index files
[Wed Feb 9 16:58:56 2011] Checking for reference FASTA file
[Wed Feb 9 16:58:56 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Feb 9 16:58:56 2011] Checking for Samtools
Samtools Version: 0.1.8
[Wed Feb 9 16:58:57 2011] Checking reads
min read length: 50bp, max read length: 54bp
format: fastq
quality scale: phred33 (default)
[Wed Feb 9 17:54:48 2011] Mapping reads against melpomene with Bowtie
[Wed Feb 9 18:16:40 2011] Joining segment hits
[Wed Feb 9 18:33:04 2011] Mapping reads against melpomene with Bowtie(1/2)
[Wed Feb 9 18:46:50 2011] Mapping reads against melpomene with Bowtie(2/2)
[Wed Feb 9 18:59:05 2011] Mapping reads against melpomene with Bowtie
[Wed Feb 9 19:25:20 2011] Joining segment hits
[Wed Feb 9 19:42:15 2011] Mapping reads against melpomene with Bowtie(1/2)
[Wed Feb 9 19:57:47 2011] Mapping reads against melpomene with Bowtie(2/2)
[Wed Feb 9 20:11:15 2011] Searching for junctions via segment mapping
[Wed Feb 9 23:00:46 2011] Searching for junctions via mate-pair closures
[Wed Feb 9 23:14:54 2011] Retrieving sequences for splices
[Wed Feb 9 23:17:05 2011] Indexing splices
[Wed Feb 9 23:49:09 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 00:14:05 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 00:36:28 2011] Joining segment hits
[Thu Feb 10 00:56:25 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 01:23:12 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 01:47:10 2011] Joining segment hits
[Thu Feb 10 02:06:56 2011] Reporting output tracks
[FAILED]
Error: Report generation failed with err = -11
Report generation failed with err = -11
I'm just starting to work with tophat. Ran it once on a single set of paired-end seqs and it finished OK. But then I got greedy and gave it 28 different sets of reads. Note that because of multiplexing samples this was not totally insane (I think) -- only 2 x 5.7e7 reads.
My current analysis goal is to use these data to generate a Cufflinks annotation for a novel butterfly genome. samples are from different individuals and tissues.
working on a linux cluster with 3TB diskspace and should have plenty of RAM/processors.
Current plan is to rerun with more modest allowance of datasets to see what happens, and/or on offending dataset (if I can fish out that detail from logs -- suggestions on that front welcome as well...)
Many Thanks, Jamie
_______________________________________
nice tophat -r 0 -i 20 -I 30000 -p 6 -g 20 --closure-search --min-closure-exon 20 --min-closure-intron 20 --min-coverage-intron 20 --min-segment-intron 20 --max-segment-intron 30000 indexes/melpomene
[Wed Feb 9 16:58:56 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Wed Feb 9 16:58:56 2011] Preparing output location edinburg_tophat_out/
[Wed Feb 9 16:58:56 2011] Checking for Bowtie index files
[Wed Feb 9 16:58:56 2011] Checking for reference FASTA file
[Wed Feb 9 16:58:56 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Feb 9 16:58:56 2011] Checking for Samtools
Samtools Version: 0.1.8
[Wed Feb 9 16:58:57 2011] Checking reads
min read length: 50bp, max read length: 54bp
format: fastq
quality scale: phred33 (default)
[Wed Feb 9 17:54:48 2011] Mapping reads against melpomene with Bowtie
[Wed Feb 9 18:16:40 2011] Joining segment hits
[Wed Feb 9 18:33:04 2011] Mapping reads against melpomene with Bowtie(1/2)
[Wed Feb 9 18:46:50 2011] Mapping reads against melpomene with Bowtie(2/2)
[Wed Feb 9 18:59:05 2011] Mapping reads against melpomene with Bowtie
[Wed Feb 9 19:25:20 2011] Joining segment hits
[Wed Feb 9 19:42:15 2011] Mapping reads against melpomene with Bowtie(1/2)
[Wed Feb 9 19:57:47 2011] Mapping reads against melpomene with Bowtie(2/2)
[Wed Feb 9 20:11:15 2011] Searching for junctions via segment mapping
[Wed Feb 9 23:00:46 2011] Searching for junctions via mate-pair closures
[Wed Feb 9 23:14:54 2011] Retrieving sequences for splices
[Wed Feb 9 23:17:05 2011] Indexing splices
[Wed Feb 9 23:49:09 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 00:14:05 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 00:36:28 2011] Joining segment hits
[Thu Feb 10 00:56:25 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 01:23:12 2011] Mapping reads against segment_juncs with Bowtie
[Thu Feb 10 01:47:10 2011] Joining segment hits
[Thu Feb 10 02:06:56 2011] Reporting output tracks
[FAILED]
Error: Report generation failed with err = -11
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