Tophat stalled error = -9

[crader]

Heya,

I've just tried out tophat on all of my QC'd RNAseq data using the the transcriptome as the index, but unfortunately its become snagged!

"Error: segment-based junction search failed with err = -9"

Can anyone offer any solutions? I'd really appreciate it! Thanks,

Craig

-------------------------------------------------------------------
$ tophat -o /home/sbica1/tophat/tophatoutput/trinity -r 50 -m 2 -p 8 /home/sbica1/tophat/L.rubellus_trinitytranscriptomeindex/L.rubellus_trinitytranscriptomeindex trimmedop010_1.fastq,trimmedop008_1.fastq,trimmedop009_1.fastq,trimmedop008_3.fastq,trimmedop009_3.fastq trimmedop010_2.fastq,trimmedop008_2.fastq,trimmedop009_2.fastq,trimmedop008_4.fastq,trimmedop009_4.fastq

[Wed Nov 9 19:57:34 2011] Beginning TopHat run (v1.0.14)
-----------------------------------------------
[Wed Nov 9 19:57:34 2011] Preparing output location /home/sbica1/tophat/tophatoutput/trinity/
[Wed Nov 9 19:57:34 2011] Checking for Bowtie index files
[Wed Nov 9 19:57:34 2011] Checking for reference FASTA file
[Wed Nov 9 19:57:34 2011] Checking for Bowtie
Bowtie version: 0.12.5.0
[Wed Nov 9 19:57:34 2011] Checking reads
seed length: 20bp
format: fastq
quality scale: phred33 (default)
[Wed Nov 9 22:21:17 2011] Mapping reads against L.rubellus_trinitytranscriptomeindex with Bowtie
[Wed Nov 9 23:51:38 2011] Joining segment hits
[Thu Nov 10 00:37:24 2011] Mapping reads against L.rubellus_trinitytranscriptomeindex with Bowtie
[Thu Nov 10 01:56:43 2011] Joining segment hits
[Thu Nov 10 02:37:40 2011] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -9

[sjm]

tophat segment error -9 due to memory problems?

@crader,

I had a number of similar problems when running tophat on a desktop machine with only 4 G of memory, and a misconfigured swap file (only 2 G in size). I don't know how big your input fastq files are, but during processing of a ~1 G fastq file with 42 nt reads, my swap file needs to grow to at least 6 G.

Scot

[biznatch]

As sjm alluded to, error -9 in Tophat likely means you ran out of memory, that's what it meant when I got that error. You'll want to get a machine with more memory and avoid having to use the swap file, as that will greatly slow down the process.