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I am currently attempting to use MaSuRCA via the superreads.pl script from StringTie.
I was hoping to understand what is the source of the problem, is it in the superreads.pl or the Quorum part. I am not certain what is the output from this in assemble.sh.
The error I am having is the following:
/stringtie-1.0.1/superreads.pl frag_1.fastq frag_2.fastq /MaSuRCA-2.3.2/ -t 24 -j 2000000000 -s 0 -r p1 -f 300 -d 50 -l Superreads.fastq -u not_assembled
Starting step 1: process input files files....
Done step 1.
Starting step 2: prepare files for assembly....
Running /MaSuRCA-2.3.2//bin/masurca sr_config.txt
Verifying PATHS...
jellyfish-2.0 OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run the assembly
Done step 2.
Starting step 3: run MaSuRCA super-read module....
[Sat Mar 7 22:16:34 CST 2015] Processing pe library reads
Average PE read length 101
choosing kmer size of 33 for the graph
MIN_Q_CHAR: 33
[Sat Mar 7 22:16:35 CST 2015] Error correct PE.
./assemble.sh: line 87: 15083 Aborted quorum_error_correct_reads -q $((MIN_Q_CHAR + 40)) --contaminant=/MaSuRCA-2.3.2/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 24 -w 10 -e 3 quorum_mer_db.jf p1.renamed.fastq --no-discard -o pe.cor --verbose > quorum.err 2>&1
Error correction of PE reads failed. Check pe.cor.log.
Assembly script did not finish running!
I was hoping to understand what is the source of the problem, is it in the superreads.pl or the Quorum part. I am not certain what is the output from this in assemble.sh.
The error I am having is the following:
/stringtie-1.0.1/superreads.pl frag_1.fastq frag_2.fastq /MaSuRCA-2.3.2/ -t 24 -j 2000000000 -s 0 -r p1 -f 300 -d 50 -l Superreads.fastq -u not_assembled
Starting step 1: process input files files....
Done step 1.
Starting step 2: prepare files for assembly....
Running /MaSuRCA-2.3.2//bin/masurca sr_config.txt
Verifying PATHS...
jellyfish-2.0 OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run the assembly
Done step 2.
Starting step 3: run MaSuRCA super-read module....
[Sat Mar 7 22:16:34 CST 2015] Processing pe library reads
Average PE read length 101
choosing kmer size of 33 for the graph
MIN_Q_CHAR: 33
[Sat Mar 7 22:16:35 CST 2015] Error correct PE.
./assemble.sh: line 87: 15083 Aborted quorum_error_correct_reads -q $((MIN_Q_CHAR + 40)) --contaminant=/MaSuRCA-2.3.2/bin/../share/adapter.jf -m 1 -s 1 -g 1 -a 3 -t 24 -w 10 -e 3 quorum_mer_db.jf p1.renamed.fastq --no-discard -o pe.cor --verbose > quorum.err 2>&1
Error correction of PE reads failed. Check pe.cor.log.
Assembly script did not finish running!
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