Question: Segmentation fault error while using GATB
0
gravatar for AriyurD
18 months ago by
AriyurD0
Germany
AriyurD0 wrote:

Dear Rayan Currently, I am developing a tool using GATB. But when I work with big datasets I am running into segmentation faults. I am using a system with 1TB of memory and the maximum memory the tool uses (including the GATB) is just 3 GB (according to Valgrind). I ran one of the tool snippets you gave in the GATB website and I still run into the same error. Here is the log file for a normal de Bruijn graph construction and node traversal:

[DSK: Collecting stats on combined_data ] 100 % elapsed: 0 min 5 sec remaining: 0 min 0 sec cpu: 611.8 % mem: [ 332, 332, 332] MB

[DSK: nb solid kmers found : 2707578473 ] 131 % elapsed: 15 min 54 sec remaining: 0 min 0 sec cpu: 320.3 % mem: [2398, 4400, 4419] MB

[MPHF: initialization ] 100 % elapsed: 56 min 30 sec remaining: 0 min 0 sec cpu: 49.6 % mem: [51556, 51556, 51556] MB

[MPHF: build hash function ] 100 % elapsed: 218 min 38 sec remaining: 0 min 0 sec cpu: 43.5 % mem: [60643, 60643, 61396] MB

[MPHF: assign values ] 99 % elapsed: 7 min 54 sec remaining: 0 min 5 sec cpu: 99.9 % mem: [42309, 42309, 61396] MB

[MPHF: populate ] 100 % elapsed: 31 min 8 sec remaining: 0 min 0 sec cpu: 82.9 % mem: [5795, 5795, 61396] MB

[Bloom: read solid kmers ] 100 % elapsed: 9 min 23 sec remaining: 0 min 0 sec cpu: 232.5 % mem: [9776, 9777, 61396] MB

[Debloom: build extension ] 99 % elapsed: 40 min 35 sec remaining: 0 min 24 sec cpu: 242.5 % mem: [9673, 9673, 61396] MB

[Debloom: finalization ] 99 % elapsed: 7 min 37 sec remaining: 0 min 4 sec cpu: 126.2 % mem: [8012, 8073, 61396] MB

[Debloom: cascading ] 100 % elapsed: 6 min 47 sec remaining: 0 min 0 sec cpu: 452.0 % mem: [8838, 8838, 61396] MB

[Graph: nb branching found : 360553065 ] 100 % elapsed: 14 min 51 sec remaining: 0 min 0 sec cpu: 1215.7 % mem: [16436, 16438, 61396] MB

Segmentation fault

Can you help me with this issue. I am using a kmer value of 21 and min abundance of 1 (which I don't want to change). My read length is 76bps

Regards Dilip

gatb • 554 views
ADD COMMENTlink modified 17 months ago by Rayan Chikhi1.2k • written 18 months ago by AriyurD0
0
gravatar for Rayan Chikhi
17 months ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

Hi, It seems that the segfault occurs at the end of graph construction. What command line did you use? Also, could you try updating to the latest GATB-core ? (released version 1.2.0) Or even, latest one here: https://github.com/GATB/gatb-core/

ADD COMMENTlink written 17 months ago by Rayan Chikhi1.2k
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