Jellyfish::file_parser::FileParserError

lovenlong · 09-17-2013, 11:51 PM

Hi, all

I try to assembled my illumina PE reads by using MaSuRCA assembler, but it aborted with the following error message:

$ ./assemble.sh
processing PE library reads 2013年 09月 18日星期三 00:04:46 CST
Average PE read length 101
choosing kmer size of 31 for the graph
running Jellyfish 2013年 09月 18日星期三 00:47:08 CST
MIN_Q_CHAR: 33
Error correction Poisson cutoff = 6
error correct PE 2013年 09月 18日星期三 02:27:13 CST
terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError'
what(): Empty input file 'pe.cor.fa'
./assemble.sh: line 63: 27070 已放弃 (core dumped) jellyfish count -p 126 -m 31 -t 8 -C -s $JF_SIZE -o k_u pe.cor.fa
terminate called after throwing an instance of 'mapped_file::ErrorMMap'
what(): Can't open file 'k_u_hash_0': No such file or directory
Estimated genome size:
Invalid uint64_t '-l' for [-n, --nb-mers=uint64]: Negative value
computing super reads from PE 2013年 09月 18日星期三 02:27:27 CST
Super reads failed, check super1.err and files in ./work1/

As far as I can see, the problem would have something to do with data trimming process. My raw reads was implemented adapter and quality trimming by using scythe and sickle, as discribed in the Assemblathon 2 paper. Then I ran the MaSuRCA.
The 'FileParserError' problem was submitted at http://seqanswers.com/forums/showthread.php?t=33688 and http://www.biostars.org/p/73067/, but seems nobody found the solution.

Also, the similary error was arised in Soapdenovo 2 as 'Seg fault' as described at http://seqanswers.com/forums/showthr...290#post106290.

I'm at a loss in finding the reason, and any guidance or suggestions would be very appreciated.

Best regards!

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09-17-2013, 11:51 PM	#1
lovenlong Member Location: Guangzhou, CN Join Date: Jan 2013 Posts: 16	Jellyfish::file_parser::FileParserError Hi, all I try to assembled my illumina PE reads by using MaSuRCA assembler, but it aborted with the following error message: $ ./assemble.sh processing PE library reads 2013年 09月 18日星期三 00:04:46 CST Average PE read length 101 choosing kmer size of 31 for the graph running Jellyfish 2013年 09月 18日星期三 00:47:08 CST MIN_Q_CHAR: 33 Error correction Poisson cutoff = 6 error correct PE 2013年 09月 18日星期三 02:27:13 CST terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError' what(): Empty input file 'pe.cor.fa' ./assemble.sh: line 63: 27070 已放弃 (core dumped) jellyfish count -p 126 -m 31 -t 8 -C -s $JF_SIZE -o k_u pe.cor.fa terminate called after throwing an instance of 'mapped_file::ErrorMMap' what(): Can't open file 'k_u_hash_0': No such file or directory Estimated genome size: Invalid uint64_t '-l' for [-n, --nb-mers=uint64]: Negative value computing super reads from PE 2013年 09月 18日星期三 02:27:27 CST Super reads failed, check super1.err and files in ./work1/ As far as I can see, the problem would have something to do with data trimming process. My raw reads was implemented adapter and quality trimming by using scythe and sickle, as discribed in the Assemblathon 2 paper. Then I ran the MaSuRCA. The 'FileParserError' problem was submitted at http://seqanswers.com/forums/showthread.php?t=33688 and http://www.biostars.org/p/73067/, but seems nobody found the solution. Also, the similary error was arised in Soapdenovo 2 as 'Seg fault' as described at http://seqanswers.com/forums/showthr...290#post106290. I'm at a loss in finding the reason, and any guidance or suggestions would be very appreciated. Best regards!