k-mer repeat count Error

[patidarr]

Hi,
I got following error:
Microsatellite Analysis for Normal-Tumor InStability (v1.0.3) python /gpfs/gsfs6/users/MoCha/patidarr/MANTIS/kmer_repeat_counter.py \ -b /data/MoCha/patidarr/MANTIS/loci.bed \ -n /gpfs/gsfs6/users/MoCha/processedDATA/714841/20170910/714841_germline~WES/714841_germline~WES.bwa.final.bam \ -t /gpfs/gsfs6/users/MoCha/processedDATA/714841/20170910/714841~288-R~KV6MF7NX7~WES/714841~288-R~KV6MF7NX7~WES.bwa.final.bam \ -o /gpfs/gsfs6/users/MoCha/processedDATA/714841/20170910/714841~288-R~KV6MF7NX7~WES/MANTIS/714841~288-R~KV6MF7NX7~WES.kmer_counts.txt \ --min-read-quality 25.0 \ --min-locus-quality 30.0 \ --min-read-length 35 \ --genome /data/MoCha/patidarr/ref/ucsc.hg19.fasta \ --threads 20 Getting repeat counts for repeat units (k-mers) ... Error with k-mer repeat count calculations; terminating program.

Could you please let me know how do I resolve it?

Thanks,
Rajesh

[rbonneville]

Is kmer_repeat_counter.py in the same folder as mantis.py?

[patidarr]

Yes they are in the same folder. I got error on a few samples of >1000 I processed.

[rbonneville]

Try running the new iss010 branch. This won't fix the problem, but should provide the information needed to identify it.

[patidarr]

Sure, I can try the new branch.

Thanks!!