Hi i'm new to MaSuRCA and got this error while trying to do my first assembly, below is the config file and the output from MaSuRCA. thanks
Thanks a lot
processing PE library reads Wed May 29 16:53:40 EDT 2013
Average PE read length 251
choosing kmer size of 175 for the graph
running Jellyfish Wed May 29 16:54:06 EDT 2013
MIN_Q_CHAR: 33
Error correction Poisson cutoff = 5
error correct PE Wed May 29 17:24:40 EDT 2013
terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError'
what(): Empty input file 'pe.cor.fa'
./assemble.sh: line 58: 610 Aborted jellyfish count -p 126 -m 31 -t 12 -C -s $JF_SIZE -o k_u pe.cor.fa
ln: creating symbolic link k_u_hash_0' to k_u_0': File exists
terminate called after throwing an instance of 'mapped_file::ErrorMMap'
what(): Can't open file k_u_hash_0:
Estimated genome size:
Invalid uint64_t '-l' for [-n, --nb-mers=uint64]: Negative value
computing super reads from PE Wed May 29 17:29:02 EDT 2013
Super reads failed, check super1.err and files in ./work1/
config.txt:
PATHS
JELLYFISH_PATH=/gpfs/home/jzr186/work/tools/bin/
SR_PATH=/gpfs/home/jzr186/work/tools/bin/
CA_PATH=/gpfs/home/jzr186/work/tools/CA/Linux-amd64/bin
END
DATA
PE= pe 300 20 /gpfs/home/jzr186/scratch/CAMP/CAMP18/JH_R1_001.fastq /gpfs/home/jzr186/scratch/CAMP/CAMP18/JH_R2_001.fastq
END
PARAMETERS
GRAPH_KMER_SIZE=auto
USE_LINKING_MATES=1
JF_SIZE=1800000000
DO_HOMOPOLYMER_TRIM=0
NUM_THREADS=12
END
4 answers
I would suggest you start your first MaSuRCA run with the test data from MaSuRCA ftp site
ftp://ftp.genome.umd.edu/pub/MaSuRCA/test_data/rhodobacter/
PE data only, then add SJ, Sanger data.
Then double-check your input data. e.g. FastqPairedEndValidator.pl
Good luck!
Update 27-07-2013
MaSuRCA finally released the config file for test data rhodobacter
ftp://ftp.genome.umd.edu/pub/MaSuRCA/test_data/rhodobacter/sr_config_Illumina_Sanger_1x.txt
Hi,
I contacted developers regarding this and they suggested that read_names does not matter during pre-processing of data. He suggested me to perform a test with my fastq file:
> file -b -i jumps.A.fastq
This gave me the results like:
text/x-python; charset=us-ascii
I emailed results to developers and they suggested that - the operating system thinks that your fastq file is a python code. This is not correct. The type should be text/plain.
The simple way to fix this:
Look at expand_fastq script under masurca bin folder and replace the line:
(text/plain*)
with
(text/*)
everything should work afterward.
After this change, I was able to run the assembler correctly with setting JF_SIZE=1800000000 value very high.
Thanks Sagar
I've been having the same problem. The test data doesn't help. My data is PE only, the paired ends have been checked, and the error happens for some genomes but not others, with no apparent pattern of read length, GC content, or anything else I can think of.
Me too, and it is so annoying!!! I thought it was a memory (RAM) problem but then I tried to re run with some libraries that worked well in past and same error.
Anyone with a solution?
Luis
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