Danqing Shen - 2022-07-05

I'm getting Aborted(core dumped) error when i'm trying to run Integrate-0.2.6 software on mRNASeq samples.

Here is the script:
Integrate fusion ./Mus_musculus.GRCm38.dna.primary_assembly.fa ./annot.VM24.txt ./bwts ./accepted_hits_sorted.bam ./unmapped.bam

Here is the output:
INTEGRATE version 0.2.6
Loading reference...
1 1 195471971
10 195471972 326166964
11 326166965 448249507
12 448249508 568378529
13 568378530 688800168
14 688800169 813702412
15 813702413 917746097
16 917746098 1015953865
17 1015953866 1110941136
18 1110941137 1201643775
19 1201643776 1263075341
2 1263075342 1445188565
3 1445188566 1605228245
4 1605228246 1761736361
5 1761736362 1913571045
6 1913571046 2063307591
7 2063307592 2208749050
8 2208749051 2338150263
9 2338150264 2462745373
MT 2462745374 2462761672
X 2462761673 2633792971
Y 2633792972 2725537669
JH584299.1 2725537670 2726490681
GL456233.1 2726490682 2726827614
JH584301.1 2726827615 2727087489
GL456211.1 2727087490 2727329224
GL456350.1 2727329225 2727557190
JH584293.1 2727557191 2727765158
GL456221.1 2727765159 2727972119
JH584297.1 2727972120 2728177895
JH584296.1 2728177896 2728377263
GL456354.1 2728377264 2728573256
JH584294.1 2728573257 2728765161
JH584298.1 2728765162 2728949350
JH584300.1 2728949351 2729131697
GL456219.1 2729131698 2729307665
GL456210.1 2729307666 2729477390
JH584303.1 2729477391 2729635489
JH584302.1 2729635490 2729791327
GL456212.1 2729791328 2729944945
JH584304.1 2729944946 2730059397
GL456379.1 2730059398 2730131782
GL456216.1 2730131783 2730198455
GL456393.1 2730198456 2730254166
GL456366.1 2730254167 2730301239
GL456367.1 2730301240 2730343296
GL456239.1 2730343297 2730383352
GL456213.1 2730383353 2730422692
GL456383.1 2730422693 2730461351
GL456385.1 2730461352 2730496591
GL456360.1 2730496592 2730528295
GL456378.1 2730528296 2730559897
GL456389.1 2730559898 2730588669
GL456372.1 2730588670 2730617333
GL456370.1 2730617334 2730644097
GL456381.1 2730644098 2730669968
GL456387.1 2730669969 2730694653
GL456390.1 2730694654 2730719321
GL456394.1 2730719322 2730743644
GL456392.1 2730743645 2730767273
GL456382.1 2730767274 2730790431
GL456359.1 2730790432 2730813405
GL456396.1 2730813406 2730834645
GL456368.1 2730834646 2730854853
JH584292.1 2730854854 2730869798
JH584295.1 2730869799 2730871774
1.39639 seconds

Loading genes...
62585 transcripts loaded.
0.239969 seconds

Loading BWTs for chromosomes...
30.6849 seconds

Handling RNA data...

Insert sizes and stds according to testing are:
684 1221

Getting graph by encompassing RNA reads...
This graph has 13111 vertexes and 95938 edges.
91.8427 seconds

Reducing Graph by removing encompassing pair with a hit in one gene mapped in BAM ...
This graph has 12734 vertexes and 94286 edges.
135.529 seconds

Getting BWTs for genes in the graph...
141.096 seconds

Adding spanning RNA reads from BAM file...
====>1000000 mapped split reads processed. 0.631552 seconds
====>2000000 mapped split reads processed. 0.587552 seconds
====>3000000 mapped split reads processed. 2.91104 seconds
====>4000000 mapped split reads processed. 3.29101 seconds
====>5000000 mapped split reads processed. 2.60176 seconds
====>6000000 mapped split reads processed. 1.92288 seconds
====>7000000 mapped split reads processed. 3.85331 seconds
====>8000000 mapped split reads processed. 7.56746 seconds
====>9000000 mapped split reads processed. 2.40554 seconds
====>10000000 mapped split reads processed. 2.81344 seconds
====>11000000 mapped split reads processed. 2.032 seconds
====>12000000 mapped split reads processed. 1.49933 seconds
====>13000000 mapped split reads processed. 4.11552 seconds
====>14000000 mapped split reads processed. 1.33245 seconds
====>15000000 mapped split reads processed. 2.62797 seconds
====>16000000 mapped split reads processed. 5.4217 seconds
====>17000000 mapped split reads processed. 2.16986 seconds
====>18000000 mapped split reads processed. 1.40829 seconds
====>19000000 mapped split reads processed. 3.76672 seconds
====>20000000 mapped split reads processed. 1.88198 seconds
====>21000000 mapped split reads processed. 4.20848 seconds
====>22000000 mapped split reads processed. 2.55888 seconds
====>23000000 mapped split reads processed. 2.85866 seconds
====>24000000 mapped split reads processed. 2.20077 seconds
====>25000000 mapped split reads processed. 10.8737 seconds
====>26000000 mapped split reads processed. 23.1145 seconds
====>27000000 mapped split reads processed. 14.9047 seconds
====>28000000 mapped split reads processed. 1.73453 seconds
====>29000000 mapped split reads processed. 3.97504 seconds
====>30000000 mapped split reads processed. 6.4368 seconds
====>31000000 mapped split reads processed. 2.12394 seconds
====>32000000 mapped split reads processed. 2.46934 seconds
====>33000000 mapped split reads processed. 0.813056 seconds
====>34000000 mapped split reads processed. 0.546816 seconds
====>35000000 mapped split reads processed. 0.582784 seconds
====>36000000 mapped split reads processed. 0.573504 seconds
====>37000000 mapped split reads processed. 0.868416 seconds
====>37035544 mapped split reads processed. 0.042048 seconds
136.309 seconds

Handle secondary split reads...
160.648 seconds

Computing number of reads on edges...
0.135936 seconds

Removing edges with too few reads...
This graph has 7602 vertexes and 23130 edges.
0.04928 seconds

Removing edges caused by repetitive encompassing reads by mapping them to both genes...
This graph has 7424 vertexes and 22586 edges.
66.1868 seconds

Estimating how repetitive of the remaining reads...
10.1914 seconds

Computing weights for edges...
0.026176 seconds

Removing edges with weight less than 2 ...
This graph has 7420 vertexes and 22577 edges.
0.0048 seconds

Getting hard cliped secondary reads' sequences ...
27.6109 seconds

Mapping soft or hard clipped reads and reads that could be partially correctly mapped from BAM
====>2560288 partially mapped reads processed. 5400.07 seconds
5400.24 seconds

Getting anchors from unaligned reads
31.0661 seconds

Mapping the unmapped reads as split reads...
====>1000000 unaligned reads processed. 545.233 seconds
====>2000000 unaligned reads processed. 544.55 seconds
====>3000000 unaligned reads processed. 571.379 seconds
====>4000000 unaligned reads processed. 542 seconds
====>5000000 unaligned reads processed. 533.885 seconds
====>6000000 unaligned reads processed. 532.924 seconds
====>7000000 unaligned reads processed. 527.376 seconds
====>8000000 unaligned reads processed. 517.576 seconds
====>9000000 unaligned reads processed. 511.158 seconds
====>10000000 unaligned reads processed. 545.621 seconds
====>11000000 unaligned reads processed. 535.211 seconds
====>11859216 unaligned reads processed. 449.077 seconds
Total time : 6355.99 seconds

Handling mapped split reads...

Here is the error:
double free or corruption (top)
/tmp/slurmd/job16843802/slurm_script: line 19: 159059 Aborted (core dumped) ./Integrate fusion ./Mus_musculus.GRCm38.dna.primary_assembly.fa ./annot.VM24.txt ./bwts ./accepted_hits_sorted.bam ./unmapped.bam

please give me some suggestions.

Regards
Danqing

 

Last edit: Danqing Shen 2022-07-05