segmentation fault and mismatch option

[Varun Gupta]

HI Everyone,
I just started using GNUMAP for RNA editing events.

I tried the following command but it gave me segmentation fault

/path to/bin/gnumap -g /path to/fasta/hg19.fa -d --print_all_sam -c 4 -o test ../trimmed.fastq

[0/1] gen_size=0, my_start=0, my_end=0
Hashing Genome...
Size of genome: 3095693983
[0/-] Converting to Vector...
    [0/-] Trying to create hash of size 1048576
Trying to create entire array of size 22890282128 (2861285266 total positions of size 8)
    [0/-] Finished create hash.
    [0/-] Stats: Total hashes is 2861285266, Longest hash is 23084752, shortest is 308, and average is 2728.734270
    [0/-] Trying to create a new genome with a size of 3095693984...Success!
[0/-] Finished Vector Conversion
Using AtoG conversion techniques
[compute-0-1005:31659] *** Process received signal ***
[compute-0-1005:31659] Signal: Segmentation fault (11)
[compute-0-1005:31659] Signal code: Address not mapped (1)
[compute-0-1005:31659] Failing at address: 0x59b0b818
[compute-0-1005:31659] [ 0] /lib64/libpthread.so.0 [0x31f920eb10]
[compute-0-1005:31659] [ 1] /opt/openmpi/lib/libopen-pal.so.0(opal_memory_ptmalloc2_int_malloc+0xd76) [0x2b1861f2dfa6]
[compute-0-1005:31659] [ 2] /opt/openmpi/lib/libopen-pal.so.0 [0x2b1861f2f2d3]
[compute-0-1005:31659] [ 3] /apps1/lib/libstdc++.so.6(_Znwm+0x1d) [0x2b1862206dbd]
[compute-0-1005:31659] [ 4] /apps1/lib/libstdc++.so.6(_Znam+0x9) [0x2b1862206ed9]
[compute-0-1005:31659] [ 5] /home/vgupta12/apps/gnumap/bin/gnumap(_ZN6Genome17make_extra_arraysEv+0x39d) [0x43517d]
[compute-0-1005:31659] [ 6] /home/vgupta12/apps/gnumap/bin/gnumap(_ZN6Genome10LoadGenomeEv+0xd4) [0x43be24]
[compute-0-1005:31659] [ 7] /home/vgupta12/apps/gnumap/bin/gnumap(main+0xa24) [0x41b5f4]
[compute-0-1005:31659] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x31f861d994]
[compute-0-1005:31659] [ 9] /home/vgupta12/apps/gnumap/bin/gnumap(__gxx_personality_v0+0x251) [0x412509]
[compute-0-1005:31659] *** End of error message ***
Segmentation fault

What could be wrong here??

Also my fastq file looks like this


@HWI-ST395_BD0W43ACXX_1:6:1101:1489:2078#ATCACG/1
AAGCTGCCAGTTGAAGAACTGT
+HWI-ST395_BD0W43ACXX_1:6:1101:1489:2078#ATCACG/1
CCCFFFFFHHHHHJJJJJJJJJ
@HWI-ST395_BD0W43ACXX_1:6:1101:1355:2082#ATCACG/1
CATAAAGTAGAAAGCACTACT
+HWI-ST395_BD0W43ACXX_1:6:1101:1355:2082#ATCACG/1
CCCFFFFDFHHHFEGHFHHIH
@HWI-ST395_BD0W43ACXX_1:6:1101:1314:2092#ATCACG/1
TAGCAGCACGTAAATATTGGCG
+HWI-ST395_BD0W43ACXX_1:6:1101:1314:2092#ATCACG/1
CCCFFFFFHHHHHIIHIJJIHJ

I only want to allow 2 mismatches when aligning to hg19 genome, but I cannot find the option to do so. Could you point me out which option does that.

Hope to hear from you soon.

Regards
Varun

[W. Evan Johnson]

CJ, 

Any intuition here?

Thanks!

Evan

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