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I'm trying to run defuse to detect gene fusions. However, I get an error when bowtie is run as part of the defuse command.
The command:
/bowtie --phred33-quals --sam-nohead -S -t -X 500 /defuse/data/defuse.cdna.fa -1 /defuse_out/jobs/reads.split.017.1.fastq -2 /defuse_out/jobs/reads.split.017.2.fastq /defuse_out/jobs/reads.split.017.cdna.pair.sam.tmp
Failure for alignjob.reads.split.017 command
Reason:
Job command with nonzero return code
Job output:
Running on cnpew18.uz.kuleuven.ac.be
Time loading reference: 00:00:01
Error reading _rstarts[] array: 1343852, 1350480
I'm running on a server, so memory should not be an issue.
Any help about what this rstart is, is really appreciated.
Thanks!
The command:
/bowtie --phred33-quals --sam-nohead -S -t -X 500 /defuse/data/defuse.cdna.fa -1 /defuse_out/jobs/reads.split.017.1.fastq -2 /defuse_out/jobs/reads.split.017.2.fastq /defuse_out/jobs/reads.split.017.cdna.pair.sam.tmp
Failure for alignjob.reads.split.017 command
Reason:
Job command with nonzero return code
Job output:
Running on cnpew18.uz.kuleuven.ac.be
Time loading reference: 00:00:01
Error reading _rstarts[] array: 1343852, 1350480
I'm running on a server, so memory should not be an issue.
Any help about what this rstart is, is really appreciated.
Thanks!