Hi forum,
I am using PBcR, following the wiki tutorial, "Correction Using Complementary High-Identity Sequences"
When I run pacBioToca to generate corrected pacbio sequences, the process stops suddenly:
<Linux-amd64>/bin/fastqToCA -libraryname illumina -technology illumina -type sanger -innie -mates illumina_forward_paired.fastq,illumina_reverse_paired.fastq > illumina.frg
<Linux-amd64>/bin/pacBioToCA -length 500 -partitions 200 -l pacbio -t 8 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out 2>&1
The last log lines are (without previous error messages):
cp asm.layout.err /apps/wgs-8.1/DATA//pacbio.correction.err
Total split bases is 0 vs 9188565 so ratio is 0
----------------------------------------END Mon Jun 9 18:29:42 2014 (0 seconds)
----------------------------------------START Mon Jun 9 18:29:42 2014
cp asm.layout.hist /apps/wgs-8.1/DATA//pacbio.correction.hist
----------------------------------------END Mon Jun 9 18:29:42 2014 (0 seconds)
----------------------------------------START Mon Jun 9 18:29:42 2014
cat `ls [0-9]*.fasta |grep trim |sort -T . -rnk1` > /apps/wgs-8.1/DATA//pacbio.fasta
I am not sure which parameter I have to edit and why the total split base are 0.
CA 8.1 is correctly installed, if I use the sample example data from the tutorial, it works.
Thanks!
I am using PBcR, following the wiki tutorial, "Correction Using Complementary High-Identity Sequences"
When I run pacBioToca to generate corrected pacbio sequences, the process stops suddenly:
<Linux-amd64>/bin/fastqToCA -libraryname illumina -technology illumina -type sanger -innie -mates illumina_forward_paired.fastq,illumina_reverse_paired.fastq > illumina.frg
<Linux-amd64>/bin/pacBioToCA -length 500 -partitions 200 -l pacbio -t 8 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out 2>&1
The last log lines are (without previous error messages):
cp asm.layout.err /apps/wgs-8.1/DATA//pacbio.correction.err
Total split bases is 0 vs 9188565 so ratio is 0
----------------------------------------END Mon Jun 9 18:29:42 2014 (0 seconds)
----------------------------------------START Mon Jun 9 18:29:42 2014
cp asm.layout.hist /apps/wgs-8.1/DATA//pacbio.correction.hist
----------------------------------------END Mon Jun 9 18:29:42 2014 (0 seconds)
----------------------------------------START Mon Jun 9 18:29:42 2014
cat `ls [0-9]*.fasta |grep trim |sort -T . -rnk1` > /apps/wgs-8.1/DATA//pacbio.fasta
I am not sure which parameter I have to edit and why the total split base are 0.
CA 8.1 is correctly installed, if I use the sample example data from the tutorial, it works.
Thanks!
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