Tophat: segment-based junction search failed with err =-11

[jdanderson]

Hello Everyone,

I was wondering if anyone has ever gotten or knows the source of the following error. I'm running Tophat (v1.3.1) on a dual core, 16GB RAM (older) desktop. The following was my command and my output while running a new paired end dataset.

tophat -o /home/johnathon/topout/ -r 209 --mate-std-dev 89 --solexa1.3-quals -p 2 -G /home/johnathon/ucsc_usable_ens_mus_ncbi37_63.gtf /home/johnathon/bowtie-0.12.7/indexes/mm9 /home/johnathon/raw_seq_data/DP_PEsequence1.txt /home/johnathon/raw_seq_data/DP_PEsequence2.txt

[Mon Jul 18 10:46:00 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Mon Jul 18 10:46:00 2011] Preparing output location /home/johnathon/topout//
[Mon Jul 18 10:46:00 2011] Checking for Bowtie index files
[Mon Jul 18 10:46:00 2011] Checking for reference FASTA file
[Mon Jul 18 10:46:00 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Jul 18 10:46:00 2011] Checking for Samtools
Samtools Version: 0.1.17
[Mon Jul 18 10:46:00 2011] Generating SAM header for /home/johnathon/bowtie-0.12.7/indexes/mm9
[Mon Jul 18 10:46:16 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Mon Jul 18 10:46:16 2011] Reading known junctions from GTF file
Left reads: min. length=107, count=28882563
Right reads: min. length=107, count=28898589
[Mon Jul 18 11:13:30 2011] Mapping left_kept_reads against mm9 with Bowtie

[Mon Jul 18 12:29:44 2011] Processing bowtie hits
[Mon Jul 18 12:52:49 2011] Mapping left_kept_reads_seg1 against mm9 with Bowtie (1/4)
[Mon Jul 18 13:53:14 2011] Mapping left_kept_reads_seg2 against mm9 with Bowtie (2/4)
[Mon Jul 18 14:55:12 2011] Mapping left_kept_reads_seg3 against mm9 with Bowtie (3/4)
[Mon Jul 18 15:56:44 2011] Mapping left_kept_reads_seg4 against mm9 with Bowtie (4/4)
[Mon Jul 18 16:20:58 2011] Mapping right_kept_reads against mm9 with Bowtie
[Mon Jul 18 17:36:52 2011] Processing bowtie hits
[Mon Jul 18 18:00:22 2011] Mapping right_kept_reads_seg1 against mm9 with Bowtie (1/4)
[Mon Jul 18 19:02:18 2011] Mapping right_kept_reads_seg2 against mm9 with Bowtie (2/4)
[Mon Jul 18 20:04:43 2011] Mapping right_kept_reads_seg3 against mm9 with Bowtie (3/4)
[Mon Jul 18 21:07:18 2011] Mapping right_kept_reads_seg4 against mm9 with Bowtie (4/4)
[Mon Jul 18 21:31:13 2011] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =-11

The following is the output of my segment_juncs.log file from the run:

segment_juncs v1.3.1 (2443)
---------------------------
Loading reference sequences...
Loading chr1...done
Loading left segment hits...
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record
Error in accessing sequence record

Any ideas on what might have caused this?

Cheers,
Johnathon