Dear all,
I am currently trying to run the MASURCA assembler with my Illumina paired-end reads. The first steps work fine but when it comes to the error correction with Quorum the program reports the following error:
quorum_error_correct_reads -q $((MIN_Q_CHAR + 40)) --contaminant=/gpfs0/global/local/masurca/3.1.3-1/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 16 -w 10 -e 3 quorum_mer_db.jf pe.renamed.fastq --no-discard -o pe.cor --verbose > quorum.err 2>&1
+ fail Error correction of PE reads failed. Check pe.cor.log.
However, there is no pe.cor.log produced. A Google research on that issue was also not very helpful. Thus, I would very much appreciate any suggestions/comments/reports.
I was also wondering where to specify the Illumina version used when running MASURCA?! Could it be that the Quorum error correction assumes the wrong Illumina version, i.e. uses the wrong quality code? Thanks a lot.
Best,
Belinda
Have u solved this probem already? I met the same problem with u now, if u have solved it, can u provide some suggestions for me? Thank u so much.
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