Question: Platypus-VCF caller - Segmentation fault (core dumped)
0
gravatar for csjlee08
12 months ago by
csjlee0810
csjlee0810 wrote:

Hello - I am trying to run a program which is a variant caller called Platypus: https://github.com/andyrimmer/Platypus

It appears to be running okay but then I get the error Segmentation fault (core dumped). I've tried to backtrace it but I am new to bioinformatics shttps://github.com/andyrimmer/Platypuso please bear with me. It said "no stack" so I am not sure where to go from here. Any help is appreciated.

greg@Genomics:/media/greg/Overflow/fastgbs/fastgbsfile/Platypus_0.8.1$ python Platypus.py callVariants --bamFiles=aln-pe.sorted.bam --refFile=adzukireferencegenome.fasta --output=VariantCalls.vcf
2018-02-12 13:34:00,698 - INFO - Beginning variant calling
2018-02-12 13:34:00,698 - INFO - Output will go to VariantCalls.vcf
2018-02-12 13:34:00,715 - INFO - Processing region NC_030637.1:0-100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:00,811 - INFO - Processing region NC_030637.1:1000000-1100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:00,955 - INFO - Processing region NC_030637.1:2000000-2100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:00,998 - INFO - Processing region NC_030637.1:3000000-3100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,047 - INFO - Processing region NC_030637.1:4000000-4100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,113 - INFO - Processing region NC_030637.1:5000000-5100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,221 - INFO - Processing region NC_030637.1:6000000-6100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,273 - INFO - Processing region NC_030637.1:7000000-7100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,326 - INFO - Processing region NC_030637.1:8000000-8100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,368 - INFO - Processing region NC_030637.1:9000000-9100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,390 - INFO - Processing region NC_030637.1:10000000-10100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,472 - INFO - Processing region NC_030637.1:11000000-11100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,504 - INFO - Processing region NC_030637.1:12000000-12100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,589 - INFO - Processing region NC_030637.1:13000000-13100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,672 - INFO - Processing region NC_030637.1:14000000-14100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:01,757 - INFO - Processing region NC_030637.1:15000000-15100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,434 - INFO - Processing region NC_030637.1:16000000-16100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,510 - INFO - Processing region NC_030637.1:17000000-17100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,552 - INFO - Processing region NC_030637.1:18000000-18100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,621 - INFO - Processing region NC_030637.1:19000000-19100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,799 - INFO - Processing region NC_030637.1:20000000-20100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,865 - INFO - Processing region NC_030637.1:21000000-21100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:02,925 - INFO - Processing region NC_030637.1:22000000-22100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,273 - INFO - Processing region NC_030637.1:23000000-23100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,328 - INFO - Processing region NC_030637.1:24000000-24100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,385 - INFO - Processing region NC_030637.1:25000000-25100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,473 - INFO - Processing region NC_030637.1:26000000-26100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,551 - INFO - Processing region NC_030637.1:27000000-27100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,603 - INFO - Processing region NC_030637.1:28000000-28100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,663 - INFO - Processing region NC_030637.1:29000000-29100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,733 - INFO - Processing region NC_030637.1:30000000-30100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,816 - INFO - Processing region NC_030637.1:31000000-31100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:03,916 - INFO - Processing region NC_030637.1:32000000-32100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:04,009 - INFO - Processing region NC_030637.1:33000000-33100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:04,102 - INFO - Processing region NC_030637.1:34000000-34100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:27,532 - INFO - Processing region NC_030637.1:35000000-35100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:27,728 - INFO - Processing region NC_030637.1:36000000-36100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:27,823 - INFO - Processing region NC_030637.1:37000000-37100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:27,912 - INFO - Processing region NC_030637.1:38000000-38100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,032 - INFO - Processing region NC_030637.1:39000000-39100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,155 - INFO - Processing region NC_030637.1:40000000-40100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,283 - INFO - Processing region NC_030637.1:41000000-41100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,407 - INFO - Processing region NC_030637.1:42000000-42100000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,496 - INFO - Processing region NC_030638.1:700000-800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,578 - INFO - Processing region NC_030638.1:1700000-1800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,611 - INFO - Processing region NC_030638.1:2700000-2800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,659 - INFO - Processing region NC_030638.1:3700000-3800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,716 - INFO - Processing region NC_030638.1:4700000-4800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,782 - INFO - Processing region NC_030638.1:5700000-5800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,812 - INFO - Processing region NC_030638.1:6700000-6800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,851 - INFO - Processing region NC_030638.1:7700000-7800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,896 - INFO - Processing region NC_030638.1:8700000-8800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,917 - INFO - Processing region NC_030638.1:9700000-9800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:28,983 - INFO - Processing region NC_030638.1:10700000-10800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:29,044 - INFO - Processing region NC_030638.1:11700000-11800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:29,069 - INFO - Processing region NC_030638.1:12700000-12800000. (Only printing this message every 10 regions of size 100000)
2018-02-12 13:34:29,091 - INFO - Processing region NC_030638.1:13700000-13800000. (Only printing this message every 10 regions of size 100000)
Segmentation fault (core dumped)
ADD COMMENTlink modified 12 months ago by Kevin Blighe37k • written 12 months ago by csjlee0810

Most likely out of RAM. How much RAM have you got? Can you monitor RAM usage via the top command in another window whilst the process runs?

ADD REPLYlink written 12 months ago by Kevin Blighe37k
1

Thanks! I managed to solve the problem by specifying nCPU=12.

ADD REPLYlink written 12 months ago by csjlee0810
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