draft_assembly aborted

[alimayy]

Hi,

Yet on another (PacBio) dataset, draft_assembly gets aborted with the error below (the dataset unfortunately is not public):

draft_assembly --db r2s3 --las r2s3.las --prefix r2s3 --config /home/amay/packages/HINGE/utils/nominal.ini --out r2s3.draft

[filter]
length_threshold = 1000;
quality_threshold = 0.23;
n_iter = 3; // filter iteration
aln_threshold = 1000;
min_cov = 5;
cut_off = 300;
theta = 300;
use_qv = true;
...
...
...
Read 0:3840 4740 5640 6540 7440 8340 9240 10140
Read 1:1736 2618 3534 4414 5332 6244 7123 8023 8923 9823
Read 2:5067 5986 6924 7814 8710 9610
Read 3:4034 4835 5688 6662 7562 8462
Read 4:2661 3473 4284 5172 6022 6882
Lane 0
[0 3840] [1 850]
Lane 1
[0 4740] [1 1736] [2 510]
Lane 2
[0 5640] [1 2618] [2 1459]
Lane 3
[0 6540] [1 3534] [2 2363]
Lane 4
[0 7440] [1 4414] [2 3237]
Lane 5
[0 8340] [1 5332] [2 4140]
Lane 6
[0 9240] [1 6244] [2 5067] [3 2244]
Lane 7
[0 10140] [1 7123] [2 5986] [3 3119]
Lane 8
[1 8023] [2 6924] [3 4034] [4 2661]
Lane 9
[1 8923] [2 7814] [3 4835] [4 3473]
Lane 10
[1 9823] [2 8710] [3 5688] [4 4284]
Lane 11
[2 9610] [3 6662] [4 5172]
Lane 12
[3 7562] [4 6022]
Lane 13
[3 8462] [4 6882]
In total 14 lanes
0
11392

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr: __pos (which is 13167) > this->size() (which is 10595)
Aborted

The strange thing is that this dataset is very similar in terms of its characteristics to other four PacBio datasets that I can run HINGE smoothly with. Any ideas?

Thanks!

[fxia22]

Thank you for reporting this bug, we are currently working on this in dev branch.

[fxia22]

Hi @alimayy, we have just updated the draft_assembly, can you try if that solves your problem? Thank you.

[alimayy]

Hi @fxia22, thanks a lot for looking into this. I actually cloned the dev branch yesterday and indeed it works without an error now.

Any ideas about #71 ? Did you guys experience it or hear about it before?