Has anybody had an trouble with Tophat 1.0.11 crashing while analyzing data that would complete normally under Tophat 1.0.10? I've got 8 FASTQ files of data where this happens.
This is from a 2.5GB FASTQ file with solexa 1.3 qualities. The run looks like this:
$ tophat -o ./lane1-crash --GFF /media/HD_2/tophat_project/mouse.gff --solexa1.3-quals -p4 m_musculus s_1_sequence.txt
[Fri Oct 16 10:11:24 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Oct 16 10:11:24 2009] Preparing output location ./lane1-crash/
[Fri Oct 16 10:11:24 2009] Checking for Bowtie index files
[Fri Oct 16 10:11:24 2009] Checking for reference FASTA file
[Fri Oct 16 10:11:24 2009] Checking for Bowtie
Bowtie version: 0.11.2.0
[Fri Oct 16 10:11:24 2009] Checking reads
seed length: 43bp
format: fastq
quality scale: --solexa1.3-quals
[Fri Oct 16 10:15:19 2009] Reading known junctions from GFF file
[Fri Oct 16 10:16:57 2009] Mapping reads against m_musculus with Bowtie
[Fri Oct 16 10:40:34 2009] Joining segment hits
[Fri Oct 16 10:45:03 2009] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -11
If I revert back to 1.0.10 this same run completes normally and I have good looking output.
This is from a 2.5GB FASTQ file with solexa 1.3 qualities. The run looks like this:
$ tophat -o ./lane1-crash --GFF /media/HD_2/tophat_project/mouse.gff --solexa1.3-quals -p4 m_musculus s_1_sequence.txt
[Fri Oct 16 10:11:24 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Fri Oct 16 10:11:24 2009] Preparing output location ./lane1-crash/
[Fri Oct 16 10:11:24 2009] Checking for Bowtie index files
[Fri Oct 16 10:11:24 2009] Checking for reference FASTA file
[Fri Oct 16 10:11:24 2009] Checking for Bowtie
Bowtie version: 0.11.2.0
[Fri Oct 16 10:11:24 2009] Checking reads
seed length: 43bp
format: fastq
quality scale: --solexa1.3-quals
[Fri Oct 16 10:15:19 2009] Reading known junctions from GFF file
[Fri Oct 16 10:16:57 2009] Mapping reads against m_musculus with Bowtie
[Fri Oct 16 10:40:34 2009] Joining segment hits
[Fri Oct 16 10:45:03 2009] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -11
If I revert back to 1.0.10 this same run completes normally and I have good looking output.
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