Error: munmap_chunk(): invalid pointer: xxxxxx

[ycl6]

I build squid from source and tried it on one of my sample, but encountered an error and it aborted:

$ ./squid-1.0/bin/squid -b Aligned.sortedByCoord.out.bam -c Chimeric.bam -G 1 -CO 1 -o squid
Reference name NR_046235        -->     25
Reference name chr1     -->     0
Reference name chr10    -->     1
Reference name chr11    -->     2
Reference name chr12    -->     3
Reference name chr13    -->     4
Reference name chr14    -->     5
Reference name chr15    -->     6
Reference name chr16    -->     7
Reference name chr17    -->     8
Reference name chr18    -->     9
Reference name chr19    -->     10
Reference name chr2     -->     11
Reference name chr20    -->     12
Reference name chr21    -->     13
Reference name chr22    -->     14
Reference name chr3     -->     15
Reference name chr4     -->     16
Reference name chr5     -->     17
Reference name chr6     -->     18
Reference name chr7     -->     19
Reference name chr8     -->     20
Reference name chr9     -->     21
Reference name chrM     -->     22
Reference name chrX     -->     23
Reference name chrY     -->     24
[Mon Aug  7 16:55:19 2017] Start reading bam file.
[Mon Aug  7 17:01:02 2017] Finish sorting Chimeric bam reads.
[Mon Aug  7 17:01:21 2017] Finish removing PCR duplicates.
[Mon Aug  7 17:01:45 2017] Building nodes. |bamdiscordant|=5085640
[Mon Aug  7 17:30:19 2017] Building nodes, finish seeding.
[Mon Aug  7 17:30:20 2017] Building nodes, finish expanding to whole genome.
[Mon Aug  7 17:30:20 2017] Building nodes, calculating read coverage for node 0.
[Mon Aug  7 17:30:23 2017] Finish calculating reads per node.
0       time=9e-06
1000000 time=366.606
2000000 time=622.674
[Mon Aug  7 17:46:56 2017] Starting building edges.
[Mon Aug  7 18:56:12 2017] Finish raw edges.
[Mon Aug  7 18:56:12 2017] Finish filtering edges from multi-aligned reads.
[Mon Aug  7 18:56:24 2017] Finish building edges.
Maximum connected component size=197
114270  18761
ILP isn't successful
0       used time 0.004122
locate all insertion place. 7.83081
finish insertion. 0.010903
0       used time 0.021042
1000    used time 3.84438
2000    used time 8.35914
3000    used time 13.1669
4000    used time 18.401
5000    used time 23.5152
locate all insertion place. 23.8758
finish insertion. 0.031942
*** Error in `./squid-1.0/bin/squid': munmap_chunk(): invalid pointer: 0x000000008bac3030 ***
Aborted

[Congm12]

Thanks for reporting that. The bug is fixed in the new version. Please try to see whether that works.

[ycl6]

@Congcong12 Thanks. I ran v1.1 without problem.

Should I be worried if squid message says ILP isn't successful? What is the consequence if ILP isn't successful? Also, the squid score ranges from single digit to >32000, is there a recommendation of a suitable cutoff of this score?

[Congm12]

That means for one connected component of genome segments, integer linear programming times out. SQUID won't predict TSV for that connected component, but result of other connected components is not affected.

There is no overall "score", but the numbers mean number of segments and edges (if I am guess what you refer to correctly). You don't need to worry about that.

[ycl6]

@Congcong12 Thanks for the explanation.