error reading rstarts[] array bowtie - defuse

Question

[lien]

Hi all,

I'm trying to run defuse, but I get an error that I don't know how to fix. The main error is error reading _rstarts[] array. Below is the complete error message (for one of the splits):

Failure for defuse command:
/defuse/scripts/alignjob.pl -c /defuse/scripts/config3.txt -j reads.split.046 -l /defuse_out/GC011094/tmp -o /defuse_out/GC011094 -n GC011094 -p /defuse_out/GC011094/jobs/reads.split.046
Reason:
Job command with nonzero return code
Job output:
Running on lien
Starting alignjob reads.split.046
Finding concordant alignments to cdna
Failure for alignjob.reads.split.046 command:
    bowtie --phred33-quals --sam-nohead -S -t -X 500 /defuse_data/defuse.cdna.fa -1 /defuse_out/GC011094/jobs/reads.split.046.1.fastq -2 /defuse_out/GC011094/jobs/reads.split.046.2.fastq /defuse_out/GC011094/jobs/reads.split.046.cdna.pair.sam.tmp
Reason:
    Job command with nonzero return code
Job output:
    Running on lien
    Time loading reference: 00:00:00
    Error reading _rstarts[] array: 1343852, 1350480
    Time loading forward index: 00:00:00
    Time searching: 00:00:00
    Overall time: 00:00:00
    Command: bowtie --phred33-quals --sam-nohead -S -t -X 500 -1 /defuse_out/GC011094/jobs/reads.split.046.1.fastq -2 /defuse_out/GC011094/jobs/reads.split.046.2.fastq /defuse_data/defuse.cdna.fa /defuse_out/GC011094/jobs/reads.split.046.cdna.pair.sam.tmp

    real    0m0.156s
    user    0m0.011s
    sys    0m0.123s
Return codes: 1
Commands failed after 1 seconds
Cleaning Up

real    0m1.197s
user    0m0.040s
sys    0m0.129s
Return codes: 25

Anyone had this error before and knows how to fix it?

Thanks!

Lien

[lien]

I forgot to mention the code I used for the defuse to get started:

./defuse.pl -c config3.txt -1 /Fastq_files/GC011094.140709.R1.fastq -2 /Fastq_files/GC011094.140709.R2.fastq -o /defuse_out/GC011094/

Working on Ubuntu 14.04. But I also tried this on a cluster, and get the exact same error.

[anik.m.1997]

Hi Lien,

I have also got the exact same error while running deFuse. Considering you have posted this problem 5 yrs ago, have you found the debug? If yes could you share them?

Thanks, Anik