basic_string::substr error when running dropEst

[wikiselev]

Hello, this may be related to #43 but I get the following error when running dropEst:

dropest -m -w -g Homo_sapiens.GRCh38.91.gtf -c indrop_v1_2.xml -o TAM103018-001_S1_L001.est Aligned.sortedByCoord.out.bam
Run: 02/04/2019 17:16:44.
RealCBs merge selected.

Start parse bams: 17:16:45.
WARNING: Can't find chromosome 'KI270729.1'
WARNING: Can't find chromosome 'KI270743.1'
WARNING: Can't find chromosome 'GL000008.2'
WARNING: Can't find chromosome 'KI270747.1'
WARNING: Can't find chromosome 'KI270722.1'
WARNING: Can't find chromosome 'KI270742.1'
WARNING: Can't find chromosome 'KI270736.1'
WARNING: Can't find chromosome 'GL000224.1'
WARNING: Can't find chromosome 'KI270719.1'
WARNING: Can't find chromosome 'KI270712.1'
WARNING: Can't find chromosome 'KI270706.1'
WARNING: Can't find chromosome 'KI270725.1'
WARNING: Can't find chromosome 'KI270715.1'
WARNING: Can't find chromosome 'KI270749.1'
WARNING: Can't find chromosome 'KI270741.1'
WARNING: Can't find chromosome 'GL000221.1'
WARNING: Can't find chromosome 'KI270716.1'
WARNING: Can't find chromosome 'KI270751.1'
WARNING: Can't find chromosome 'KI270519.1'
WARNING: Can't find chromosome 'GL000214.1'
WARNING: Can't find chromosome 'KI270708.1'
WARNING: Can't find chromosome 'KI270730.1'
WARNING: Can't find chromosome 'KI270438.1'
WARNING: Can't find chromosome 'KI270737.1'
WARNING: Can't find chromosome 'KI270738.1'
WARNING: Can't find chromosome 'KI270748.1'
WARNING: Can't find chromosome 'KI270435.1'
WARNING: Can't find chromosome 'GL000208.1'
WARNING: Can't find chromosome 'KI270538.1'
WARNING: Can't find chromosome 'KI270756.1'
WARNING: Can't find chromosome 'KI270739.1'
WARNING: Can't find chromosome 'KI270746.1'
WARNING: Can't find chromosome 'KI270753.1'
WARNING: Can't find chromosome 'KI270589.1'
WARNING: Can't find chromosome 'KI270735.1'
WARNING: Can't find chromosome 'KI270714.1'
WARNING: Can't find chromosome 'KI270732.1'
WARNING: Can't find chromosome 'KI270754.1'
WARNING: Can't find chromosome 'KI270710.1'
WARNING: Can't find chromosome 'KI270717.1'
WARNING: Can't find chromosome 'KI270724.1'
WARNING: Can't find chromosome 'KI270720.1'
WARNING: Can't find chromosome 'KI270723.1'
WARNING: Can't find chromosome 'KI270718.1'
WARNING: Can't find chromosome 'KI270740.1'
WARNING: Can't find chromosome 'KI270579.1'
WARNING: Can't find chromosome 'KI270752.1'
WARNING: Can't find chromosome 'KI270512.1'
WARNING: Can't find chromosome 'KI270582.1'
WARNING: Can't find chromosome 'KI270362.1'
WARNING: Can't find chromosome 'KI270593.1'
WARNING: Can't find chromosome 'KI270508.1'
ERROR: can't find chromosome, id: -1
Aligned.sortedByCoord.out.bam: 3189315 total reads; 42.4% intergenic; 24.6% touch exon; 32.9% touch intron; 3.1% touch not annotated re
Bams parsed: 17:18:08.

2038 CBs with more than 20 genes
top CBs:
614     TGATCGACACCGGCGGTTT
608     TGAAAATGTCGTTAAGCGT
596     AGGGAACGACGGCTTAC
587     AGCTTTCCATTAAGCGT
578     AGGGAACGAGCGCATTC
571     TGATGTCTTTCCAATTAGT
571     TGAACTAGCCACCCTTGGT
546     TGCCTCACTTGTTTAC
540     TGAGGTTTCTCAGAACGGG

Start merge: 17:18:08.
Merge initialized: 17:18:08.
basic_string::substr: __pos (which is 18446744073709547612) > this->size() (which is 18)

Does not look like a memory issue. Do you know what it could be? Many thanks in advance!

[lucacozzuto]

it looks like a problem with coordinates?

[droplet-lab]

@lucacozzuto and @wikiselev did you guys perhaps figure out where this comes from? Thanks!

[lucacozzuto]

I had a similar error caused by an empty line at the end of my GTF.