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gymrek-lab / LongTR

Tandem repeat genotyping with long reads
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LongTR v1.1 segfaults after "Processing flanking sequences" #19

Open davidlougheed opened 4 days ago

davidlougheed commented 4 days ago

Hello, When I run the latest LongTR v1.1, I get an exit code 11 (segfault) almost immediately after calling begins, right after Processing flanking sequences:

...
Processing region chr1 16710 16743
29 reads overlapped region, of which 
    0 were hard clipped
    0 had an 'N' base call
    6 had low MAPQ
    1 had low base quality scores
    0 did not span the STR
    0 did not have a unique mapping
    22 PASSED ALL FILTERS
Phased SNPs add info for 0 out of 22 reads and 0 out of 1 samples
Trimming reads
Generating candidate haplotypes
    GTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGA GCTGGGGGTGGTGGTGGGGGCGGTGGGGGTGGT GTTAGTACCCCATCTTGTAGGTCTGAAACACAAAG 
Added 0 inexact haplotypes generated by POA
Aligning reads to each candidate haplotype
Processing flanking sequences

At which point the job exits with code 11 indicating a segmentation fault. This did not happen in version 1.0.

heliziii commented 4 days ago

Hi David,

Do you have --skip-assembly in your list of parameters? If so, please remove it, I decided to remove this option as it was causing so much confusion. Otherwise, please share your script so I can look further.

Thanks, Helia

davidlougheed commented 4 days ago

ah yes, that is in my list of parameters, I did not realize the parameters had changed. I'll try running it without.