unfortunately it seems as if your fix has broken something.
I have run a simulation as described above, but this time for a whole WES bed file on all major chromosomes and split into 30 processes:
Three processes exited prematurely with the following error messages:
... 82% 83% Index error when attempting to find cigar string. 22318 22318 (22226, 22318) 0 193 182 ... 5% 6% Index error when attempting to find cigar string. 22309 22309 (22172, 22309) 1 238 226 ... 22% 23% Index error when attempting to find cigar string. 22315 22315 (22223, 22315) 0 193 182
I then ran the exact same job again, but this time using the old version before your recent fix and it completed successfully.
ju-mu
commented
5 years ago
Hi,
unfortunately it seems as if your fix has broken something. I have run a simulation as described above, but this time for a whole WES bed file on all major chromosomes and split into 30 processes:
python genReads.py -r test.fa -M 0.002 -R 101 -c 200 -o testdir/testprefix --vcf -t test.bed -e mytest_errorModel.p -m models/MutModel_CLLE-ES_ICGC.p --pe-model mytest_fraglen.p --gc-model mytest_gcBiasModel.p --bam -v mytest_test.vcf --rng 999 --job 1 30Three processes exited prematurely with the following error messages:
... 82% 83% Index error when attempting to find cigar string. 22318 22318 (22226, 22318) 0 193 182... 5% 6% Index error when attempting to find cigar string. 22309 22309 (22172, 22309) 1 238 226... 22% 23% Index error when attempting to find cigar string. 22315 22315 (22223, 22315) 0 193 182I then ran the exact same job again, but this time using the old version before your recent fix and it completed successfully.
Could you have a look?
Many thanks!
Originally posted by @ju-mu in https://github.com/zstephens/neat-genreads/issues/56#issuecomment-474870548