Newbler template bug???
Reported by john.mccallum (at plantandfood) | April 1st, 2011 @ 01:16 AM
[Cfljam@pgenome 40.assemble]$ moa new newbler -t 'assemble DH
skim reads' Created a Moa newbler job
[Cfljam@pgenome 40.assemble]$ moa set input input:
$ ../00.raw/MID6.sff [Cfljam@pgenome 40.assemble]$ moa show input
../00.raw/MID6.sff
largecontig_cutoff
library_name $(shell echo basename $(CURDIR)
| sed
"s/[ \///\/]//g" )
mid_configuration
mids
min_identity
postcommand
precommand
title assemble DH skim reads
[Cfljam@pgenome 40.assemble]$ moa set library_name
library_name:
$ DHSkim [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
Moa Error running run (<1 sec)
[Cfljam@pgenome 40.assemble]$ pwd
/data/moa/onion/20.genomic.sequencing/40.assemble [Cfljam@pgenome
40.assemble]$ [ pgenome ][
Comments and changes to this ticket
-
MF April 1st, 2011 @ 01:25 AM
- State changed from new to resolved
(from [57b913d674666c2090e56e36ae583056fa7fe16d]) fixed newbler bug - removed -consed parameter [#13 state:resolved] https://github.com/mfiers/Moa/commit/57b913d674666c2090e56e36ae5830...
-
MF April 1st, 2011 @ 06:39 AM
(from [d96e03465d46bef27c7cf5fb7c2f430b84438efb]) Merge branch 'moa.0.10' of git@ssh.github.com:mfiers/Moa into moa.0.10
- 'moa.0.10' of git@ssh.github.com:mfiers/Moa: fixed newbler bug - removed -consed parameter [#13 state:resolved] updated the README file [#12 state:resolved] https://github.com/mfiers/Moa/commit/d96e03465d46bef27c7cf5fb7c2f43...
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Referenced by
- 13 Newbler template bug??? (from [57b913d674666c2090e56e36ae583056fa7fe16d]) fixed n...
- 14 Newbler template bug V2.0 ??? [#13 state:resolved]
- 12 Test Ticket 'moa.0.10' of git@ssh.github.com:mfiers/Moa: fixed newble...
- 13 Newbler template bug??? 'moa.0.10' of git@ssh.github.com:mfiers/Moa: fixed newble...