Hi all,
Has anyone else run into this error when running TopHat-Fusions
"Error: Splice sequence retrieval failed with err =-11"
I am using the latest beta version of TopHat-Fusions (0.1.0) and a version compiled from source. The exact command I am running is:
This is not some random one library error. It's happened in 5 libraries. I've emailed the creators of it, but haven't got any replies. So any help or suggestions would be greatly appreciated. Below is the full log of the error. Thanks.
Has anyone else run into this error when running TopHat-Fusions
"Error: Splice sequence retrieval failed with err =-11"
I am using the latest beta version of TopHat-Fusions (0.1.0) and a version compiled from source. The exact command I am running is:
Code:
tophat-fusion --solexa1.3-quals --library-type fr-unstranded -o A05247 -p 2 --allow-indels --no-coverage-search -r 136 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 -G ucsc.gtf bowtie_indices/hg19 reads.1.fastq reads.2.fastq
[Tue Nov 8 09:58:56 2011] Beginning TopHat run (v0.1.0 (Beta))
-----------------------------------------------
[Tue Nov 8 09:58:56 2011] Preparing output location /share/lustre/gascoyne/WTSS/HL_CELL_LINES/tophat_fusions/A05247/
[Tue Nov 8 09:58:56 2011] Checking for Bowtie index files
[Tue Nov 8 09:58:56 2011] Checking for reference FASTA file
[Tue Nov 8 09:58:56 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 8 09:58:56 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Nov 8 09:59:05 2011] Checking reads
min read length: 76bp, max read length: 76bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Tue Nov 8 11:18:00 2011] Reading known junctions from GTF file
[Tue Nov 8 11:41:07 2011] Mapping reads against hg19 with Bowtie
[Tue Nov 8 16:50:08 2011] Joining segment hits
[Tue Nov 8 17:23:26 2011] Mapping reads against hg19 with Bowtie (1/3)
[Tue Nov 8 21:08:36 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 00:47:34 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 03:33:56 2011] Mapping reads against hg19 with Bowtie
[Wed Nov 9 08:08:31 2011] Joining segment hits
[Wed Nov 9 08:42:17 2011] Mapping reads against hg19 with Bowtie (1/3)
[Wed Nov 9 12:58:22 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 17:26:48 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 21:03:10 2011] Searching for junctions via segment mapping
[Thu Nov 10 01:46:20 2011] Retrieving sequences for splices
[FAILED]
Error: Splice sequence retrieval failed with err =-11
-----------------------------------------------
[Tue Nov 8 09:58:56 2011] Preparing output location /share/lustre/gascoyne/WTSS/HL_CELL_LINES/tophat_fusions/A05247/
[Tue Nov 8 09:58:56 2011] Checking for Bowtie index files
[Tue Nov 8 09:58:56 2011] Checking for reference FASTA file
[Tue Nov 8 09:58:56 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 8 09:58:56 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Nov 8 09:59:05 2011] Checking reads
min read length: 76bp, max read length: 76bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Tue Nov 8 11:18:00 2011] Reading known junctions from GTF file
[Tue Nov 8 11:41:07 2011] Mapping reads against hg19 with Bowtie
[Tue Nov 8 16:50:08 2011] Joining segment hits
[Tue Nov 8 17:23:26 2011] Mapping reads against hg19 with Bowtie (1/3)
[Tue Nov 8 21:08:36 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 00:47:34 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 03:33:56 2011] Mapping reads against hg19 with Bowtie
[Wed Nov 9 08:08:31 2011] Joining segment hits
[Wed Nov 9 08:42:17 2011] Mapping reads against hg19 with Bowtie (1/3)
[Wed Nov 9 12:58:22 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 17:26:48 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 21:03:10 2011] Searching for junctions via segment mapping
[Thu Nov 10 01:46:20 2011] Retrieving sequences for splices
[FAILED]
Error: Splice sequence retrieval failed with err =-11
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