Segmentation fault when fruit.x.las empty

[mictadlo]

Hi, Hinge runs in Segmentation fault when one of many x.las is empty

[2017-03-16 09:18:59.081] [log] [info] name of las: fruit.16.las
[2017-03-16 09:18:59.160] [log] [info] Load alignments from fruit.16.las
[2017-03-16 09:18:59.160] [log] [info] # Alignments: 127553882
[2017-03-16 09:20:34.739] [log] [info] # reads: 34130
[2017-03-16 09:20:34.739] [log] [info] # active reads: 1391/34130
[2017-03-16 09:20:34.739] [log] [info] Input data finished, part 16/30
[2017-03-16 09:21:13.952] [log] [info] kept 781263/127553882 overlaps,  324911/53119069 rev_overlaps in part 16/30
[2017-03-16 09:21:13.953] [log] [info] index finished
[2017-03-16 09:21:17.181] [log] [info] name of las: fruit.17.las
[2017-03-16 09:21:17.197] [log] [info] Load alignments from fruit.17.las
[2017-03-16 09:21:17.197] [log] [info] # Alignments: 0
/work/lorencm/apps/HINGE/inst/bin/hinge: line 8: 28975 Segmentation fault      hinging "$@"

Michal

[fxia22]

this is a rare case. One section of the DB has no alignments at all. Can you LAshow fruit.17.las and LAshow fruit.17.las | wc to confirm this is the problem? Thanks!

[mictadlo]

The file size was 0 and I deleted it.

[govinda-kamath]

What about fruit.18.las (or later parts)? Were they empty as well?

[mictadlo]

Yes, they empty as well

[govinda-kamath]

It looks like something went wrong with your DAligner run then there then. Is this directly though DAligner or did you run an LAsplit?

[mictadlo]

I did

DBsplit -x500 -s100 fruit
HPC.daligner -t10 fruit | csh -v
LAmerge fruit.las fruit.*.las
rm fruit.*.las # we only need fruit.las
DASqv -c100 fruit fruit.las
LAsplit -v fruit.# 30 < fruit.las

[mictadlo]

p.s.

> LAsplit -v fruit.# 30 < fruit.las
  Distributing 3826712020 la's
  Split off fruit.1: 127568215 la's
  Split off fruit.2: 127552925 la's
  Split off fruit.3: 127555045 la's
  Split off fruit.4: 127557223 la's
  Split off fruit.5: 127557995 la's
  Split off fruit.6: 127560592 la's
  Split off fruit.7: 127549461 la's
  Split off fruit.8: 127570594 la's
  Split off fruit.9: 127550190 la's
  Split off fruit.10: 127553482 la's
  Split off fruit.11: 127559188 la's
  Split off fruit.12: 127554286 la's
  Split off fruit.13: 127555785 la's
  Split off fruit.14: 127563615 la's
  Split off fruit.15: 127554589 la's
  Split off fruit.16: 127553882 la's
  Split off fruit.17: 0 la's
  Split off fruit.18: 0 la's
  Split off fruit.19: 0 la's
  Split off fruit.20: 0 la's
  Split off fruit.21: 0 la's
  Split off fruit.22: 0 la's
  Split off fruit.23: 0 la's
  Split off fruit.24: 0 la's
  Split off fruit.25: 0 la's
  Split off fruit.26: 0 la's
  Split off fruit.27: 0 la's
  Split off fruit.28: 0 la's
  Split off fruit.29: 0 la's
  Split off fruit.30: 0 la's

[govinda-kamath]

I see. Just deleting the las from 17 onwards should be return the right answer. We will add checks to the code so that it recognises that things are empty in an automated manner.

[govinda-kamath]

@mictadlo Can you give me the output of the following command in your directory?

ls -l fruit.[1-3][0-9].las

[mictadlo]

ls -l fruit.[1-3][0-9].las
-rw-rw---- 1 lorencm lorencm 10736406520 Mar 14 08:40 fruit.10.las
-rw-rw---- 1 lorencm lorencm 10755072894 Mar 14 08:41 fruit.11.las
-rw-rw---- 1 lorencm lorencm 10763477598 Mar 14 08:41 fruit.12.las
-rw-rw---- 1 lorencm lorencm 10764588858 Mar 14 08:42 fruit.13.las
-rw-rw---- 1 lorencm lorencm 10790002160 Mar 14 08:43 fruit.14.las
-rw-rw---- 1 lorencm lorencm 10769385544 Mar 14 08:43 fruit.15.las
-rw-rw---- 1 lorencm lorencm 10746384190 Mar 14 08:44 fruit.16.las

[govinda-kamath]

I actually wanted to know if the parts 17 and above are empty (as in size 0) files. Do you know if they were empty?

[mictadlo]

> ls -l fruit.[1-3][0-9].las
-rw-rw---- 1 lorencm lorencm 10736406520 Mar 17 13:05 fruit.10.las
-rw-rw---- 1 lorencm lorencm 10755072894 Mar 17 13:06 fruit.11.las
-rw-rw---- 1 lorencm lorencm 10763477598 Mar 17 13:07 fruit.12.las
-rw-rw---- 1 lorencm lorencm 10764588858 Mar 17 13:07 fruit.13.las
-rw-rw---- 1 lorencm lorencm 10790002160 Mar 17 13:08 fruit.14.las
-rw-rw---- 1 lorencm lorencm 10769385544 Mar 17 13:09 fruit.15.las
-rw-rw---- 1 lorencm lorencm 10746384190 Mar 17 13:09 fruit.16.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.17.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.18.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.19.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.20.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.21.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.22.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.23.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.24.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.25.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.26.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.27.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.28.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.29.las
-rw-rw---- 1 lorencm lorencm          12 Mar 17 13:09 fruit.30.las

[govinda-kamath]

This has been resolved in the latest version I think.