tophat error: Report generation failed with err = -11

[Bioboatr]

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

[Bioboatr]

Okay, found at least one problem I was having. My data are in Illumina1.3 quality scores, which I failed to specify. Should have used '--solexa1.3-quals'. Hope this is the reason for the fail. Seems likely...

If at first you don't succeed...

[Bioboatr]

... you keep on failing until you figure out the problem. Which I have not. I reran with correct quality scoring specified and suffered the same fate. tophat err = -11 ? Anyone?

jamie

[Bioboatr]

Splitting the dataset into 5 subsets and running each of those separately did not cause the same error. All 5 runs finished up just fine. So there is clearly something problematic about combining either that volume of data or that many different files... Don't know which.

[Emilie]

Hi Jamie,

I have obtained the same error message with human paired-end data (~140 million of paired-end reads). It seems to come from the high number of reads, as it has worked previously with <100 million of paired-end reads. I have splitted the dataset to see if it works.
How many reads do you have ?

Emilie

[Emilie]

It works when I split my dataset in 3 chunks (~50 million of paired-end reads per chunk). It seems most probably that there is an issue with the size of the dataset.

[Bioboatr]

I agree... seems the most logical explanation for the run fail... but I'm a biologist and new to this, so hard to say for sure...

Good luck,

jamie

[flobpf]

Tmp directory too big

I am getting this error too. I believe (atleast in my case) that it is due to disk getting full with the tmp directory. Just before giving this error, tophat says:

sort: close failed: -: No space left on device

Errors are:

Report generation failed with err = -11

or

Error: Report generation failed with err = 1