empty .vcf

[Sophie Blanc]

Hi everyone,

I have a problem that I can't figure out.. Here is my command (from the FastGBS program) :

Platypus.py callVariants --bamFiles=../results/List_bam     --nCPU=8 --minMapQual=20 --minBaseQual=20     --minGoodQualBases=5 --badReadsThreshold=10     --rmsmqThreshold=20 --abThreshold=0.01 --maxReadLength=250  --hapScoreThreshold=20     --trimAdapter=0 --maxGOF=20     --minReads=2 --genIndels=1 --minFlank=5     --sbThreshold=0.01 --scThreshold=0.95 --hapScoreThreshold=15     --filterDuplicates=0     --filterVarsByCoverage=0 --filteredReadsFrac=0.7 --minVarFreq=0.002     --mergeClusteredVariants=0 --filterReadsWithUnmappedMates=0     --refFile=../refgenome/PN12Xv2_chloro_mito.fa     --logFileName=FastGBS_platypus_log.txt     --output=FastGBS_platypus.vcf

Platypus runs fine and gives me no error message. But I get an empty .vcf, stopped in the middle of the header...

Here are the messages I have in my terminal (knowing my reference genome has 19 chromosomes + mito + chloro):

Search the variants with platypus

2017-10-03 17:03:34,810 - INFO - Beginning variant calling

2017-10-03 17:03:34,811 - INFO - Output will go to FastGBS_platypus.vcf

2017-10-03 17:03:41,561 - INFO - Processing region Vv_chloroplast:0-100000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:41,647 - INFO - Processing region Vv_chloroplast:100000-160928. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:41,733 - INFO - Processing region Vv_mitochondrion:0-100000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:41,820 - INFO - Processing region Vv_mitochondrion:100000-200000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:41,906 - INFO - Processing region Vv_mitochondrion:200000-300000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:41,992 - INFO - Processing region Vv_mitochondrion:300000-400000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,079 - INFO - Processing region Vv_mitochondrion:400000-500000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,167 - INFO - Processing region Vv_mitochondrion:500000-600000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,253 - INFO - Processing region Vv_mitochondrion:600000-700000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,343 - INFO - Processing region Vv_mitochondrion:700000-773279. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,431 - INFO - Processing region chr1:0-100000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,518 - INFO - Processing region chr1:100000-200000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,603 - INFO - Processing region chr1:200000-300000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,691 - INFO - Processing region chr1:300000-400000. (Only printing this message every 10 regions of size 100000)

2017-10-03 17:03:42,773 - INFO - Merging output VCF file(s) into final file FastGBS_platypus.vcf

2017-10-03 17:03:42,775 - INFO - Finished merging VCF file(s)

2017-10-03 17:03:42,775 - INFO - Finished variant calling

and that's it... And in the log file there is no error message.

Does anyone would have an idea of what's happening?

Thanks!!

Sophie

[Andy Rimmer]

Hi Sophie,

That's unusual. If there are no errors, but Platypus is skipping whole chromosomes then something is very wrong. Can you try running with --nCPU=1 and see if that makes any difference? If that doesn't give any useful output then try setting --verbosity=3 and check the

log file for anything weird (or post it here).

How many BAM files are there in the list? 

Kind regards,

Andy

Sophie

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[Sophie Blanc]

Dear Andy and all,

Well the problem I have looks serious, because I tried running a very simple command, and I get a "segmentation fault" anyway. Here is my command :

python /cm/shared/apps/Platypus_0.8.1/Platypus.py callVariants --refFile=./refgenome/PN12Xv2.fa --bamFiles=./data/H3T5WBBXX_1_BC01.sort.bam --verbosity=5 -o test_platypus.vcf

Even if I do an "export path" for C_INCLUDE, LIBRARY and LD_LIBRARY, I get a "segmentation fault"...

I don't understand how to resolve this.

Here is the error I get (basically the genome I work on has 19 chromosomes) :

"2017-10-11 10:08:11,913 - INFO - Processing region chr1:0-100000. (Only printing this message every 10 regions of size 100000)

Segmentation fault"

Would anyone have an idea of what could be wrong?

Sophie

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