Newbler template bug V2.0 ???
Reported by john.mccallum (at plantandfood) | April 1st, 2011 @ 01:32 AM
[Cfljam@pgenome 40.assemble]$ pwd
/data/moa/onion/20.genomic.sequencing/40.assemble [Cfljam@pgenome
40.assemble]$ ls -la total 12
drwxrwxr-x 3 Cfljam users 4096 Apr 1 14:31 .
drwxrwxrwx 9 Cfljam users 4096 Apr 1 14:14 ..
drwxrwxr-x 4 Cfljam users 4096 Apr 1 14:31 .moa
-rw-rw-r-- 1 Cfljam users 0 Apr 1 14:31 singletons.lst
[Cfljam@pgenome 40.assemble]$ moa show input ../00.raw/MID6.sff
largecontig_cutoff
library_name DHSkim
mid_configuration
mids
min_identity
postcommand awk '$2=="Singleton" {print $1}'
DHSkim/454ReadStatus.txt > singletons.lst
precommand
title assemble DH skim reads
[Cfljam@pgenome 40.assemble]$ moa run Executing
Input files ../00.raw/MID6.sff
runAssembly -ace -o . -consed ../00.raw/MID6.sff
Error: Options -ace, -noace, -acedir, -consed and -consed16 are
mutually exlusive.
Usage: runAssembly [-o projdir] [-nrm] [-p (sfffile |
[regionlist:]analysisDir)]... (sfffile |
[regionlist:]analysisDir)...
Traceback (most recent call last):
File "/opt/moa10/bin/fastaInfo", line 155, in
for name, seq in fastareader(inp):
File "/opt/moa10/bin/fastaInfo", line 87, in fastareader
F = open(f, 'r')
IOError: [Errno 2] No such file or directory:
'454LargeContigs.fna'
make: *** [454LargeContigs.all.png] Error 1
awk: cmd. line:1: fatal: cannot open file
`DHSkim/454ReadStatus.txt' for reading (No such file or
directory)
Moa Error running run (<1 sec)
[Cfljam@pgenome 40.assemble]$
Comments and changes to this ticket
-
MF April 1st, 2011 @ 01:40 AM
- State changed from new to resolved
John - this is a new 'feature' :)
templates are now copied in the .moa directory - this ultimately improves
reproducibility of a pipeline as changing templates are not automatically
part of the pipeline. But it does mean that you have to run 'moa refresh'
after a template update that you want. I never told you this.Oh - btw you could have opened the other ticket / that would have been
neater :)[#13 state:resolved]
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