Platypus-VCF caller - Segmentation fault (core dumped)
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6.2 years ago
csjlee08 ▴ 10

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)
gbs next-gen variant calling Platypus • 1.7k views
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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?

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

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