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Old 02-17-2012, 09:21 AM   #1
shuang
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Location: IL

Join Date: Jul 2011
Posts: 100
Default errors with PacBioToCA in Celera

I'm learning to use Celera to assemble PacBio sequences. However, I can NOT make pacBioToCA working.

I'm stock with pacBioToCA command when I'm following the example exercise on http://sourceforge.net/apps/mediawik...tle=PacBioToCA

./fastqToCA -libraryname illumina -technology illumina -type sanger -innie -reads illumina.fastq > illumina.frg

java convertFastaAndQualToFastq wgs-7.0/Linux-amd64/bin/sampleData/pacbio.filtered_subreads.fasta > wgs-7.0/Linux-amd64/bin/sampleData/pacbio.filtered_subreads.fastq

./pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg


Then, here came an error message:

Running with 16 threads and 200 partitions
AMOS binaries: bank-transact not found in
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Old 03-06-2012, 07:40 AM   #2
fturner
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Location: Edinburgh

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Default

have you installed AMOS libaries (see other requirements at http://sourceforge.net/apps/mediawik...ng_from_Source ) ? This error went away when I did this and added the directory src/Bank in the the AMOs directory to my path.
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Old 03-08-2012, 08:42 AM   #3
shuang
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After I set the path pointing to amos directory, the problem was solved. Thanks!
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