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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Error was value too large to convert to int #73

Open anubhabkhan opened 6 years ago

anubhabkhan commented 6 years ago

Hi,

I tried to run platypus using the following command: python Platypus.py callVariants --bamFiles=bamfiles --output=variatnts_platy.vcf --refFile=loci.fa --maxReads=5000000000 --bufferSize=10000

but i get error: 2018-02-07 12:20:58,894 - INFO - Beginning variant calling 2018-02-07 12:20:58,896 - INFO - Output will go to variatnts_platy.vcf 2018-02-07 12:20:59,090 - INFO - Processing region EU153.1:0-10000. (Only printing this message every 10 regions of size 10000) 2018-02-07 12:20:59,095 - ERROR - Exception in region EU153.1:0-10000. Error was value too large to convert to int 2018-02-07 12:20:59,095 - WARNING - Region EU153.1:0-10000 will be skipped 2018-02-07 12:20:59,095 - ERROR - Exception in region EU153.1:10000-20000. Error was value too large to convert to int 2018-02-07 12:20:59,095 - WARNING - Region EU153.1:10000-20000 will be skipped 2018-02-07 12:20:59,096 - ERROR - Exception in region EU153401.1:20000-30000. Error was value too large to convert to int 2018-02-07 12:20:59,096 - WARNING - Region EU153.1:20000-30000 will be skipped 2018-02-07 12:20:59,096 - ERROR - Exception in region EU153401.1:30000-40000. Error was value too large to convert to int 2018-02-07 12:20:59,096 - WARNING - Region EU153.1:30000-40000 will be skipped 2018-02-07 12:20:59,097 - ERROR - Exception in region EU153.1:40000-50000. Error was value too large to convert to int 2018-02-07 12:20:59,097 - WARNING - Region EU153.1:40000-50000 will be skipped 2018-02-07 12:20:59,097 - ERROR - Exception in region EU153.1:50000-60000. Error was value too large to convert to int 2018-02-07 12:20:59,097 - WARNING - Region EU153.1:50000-60000 will be skipped 2018-02-07 12:20:59,097 - ERROR - Exception in region EU153.1:60000-70000. Error was value too large to convert to int 2018-02-07 12:20:59,098 - WARNING - Region EU153.1:60000-70000 will be skipped 2018-02-07 12:20:59,098 - ERROR - Exception in region EU153.1:70000-80000. Error was value too large to convert to int 2018-02-07 12:20:59,098 - WARNING - Region EU153.1:70000-80000 will be skipped

can someone please help

tdelhomme commented 6 years ago

Why the genomic regions are in the form EU153.1:start-end? Not sure is the reason why you get an error.

anubhabkhan commented 6 years ago

any suggestions as to how to fix this? It's just the name of the reference genes. Does that really matter?

tdelhomme commented 6 years ago

I do not really know is this matters or not, but I know that region must be in the format CHR:start-end so maybe be there is a mistake in the fasta file, and maybe platypus does not accept that.

MaximilianStammnitz commented 4 years ago

Hi @anubhabkhan, @tdelhomme,

Since I've just come across the exact same issue as you, better late than never: the "max.int" value for Shell commands is 2,147,483,647. You are currently exceeding this number by specifying up to 5,000,000,000 reads, and Platypus therefore can't handle it as an input. One way around this coverage limitation is to reduce the window size and specify only up to ~2,1 Billion reads, or to downsample your BAM file otherwise.

Best, Max