gsMapper template problem
Reported by john.mccallum (at plantandfood) | April 11th, 2011 @ 12:08 AM | in v1.1
gsMapper is broken and I dont know why
[Cfljam@pgenome 20.gsMapper]$ pwd
/data/moa/onion/11.Colour_CGs/10.AcMyb1/20.gsMapper [Cfljam@pgenome
20.gsMapper]$ moa refresh [Cfljam@pgenome 20.gsMapper]$ moa show
annotation NR reads
min_overlap_ident 90
min_overlap_len 40
name NR reads
postcommand
precommand
project
reference_fasta ../00.raw_data/gsAcMyb1_consensus.fasta
sfffile
/data/moa/onion/15.cdna.sequencing/00.raw/Nasik_GLX_reads.sff
title map reads to AcMyb
[Cfljam@pgenome 20.gsMapper]$ moa clean [Cfljam@pgenome
20.gsMapper]$ moa run Traceback (most recent call last):
File "/opt/moa10/bin/moa", line 269, in
rc = run(job, command)
File "/opt/moa10/bin/moa", line 169, in run
plugins.run("pre%s" % execNow.capitalize())
File "/opt/moa10/lib/python/moa/plugin/init.py", line 73, in run
rv['p'] = getattr(self[p], command)(self.sysConf)
File "/opt/moa10/lib/python/moa/plugin/status.py", line 173, in preRun
status = _getStatus(data.job)
File "/opt/moa10/lib/python/moa/plugin/status.py", line 94, in _getStatus
otherPid = _getPid()
TypeError: _getPid() takes exactly 1 argument (0 given)
[Cfljam@pgenome 20.gsMapper]$ [ pgenome ][
Comments and changes to this ticket
-
MF April 28th, 2011 @ 12:40 AM
- Milestone changed from “v1.0” to “v1.1”
- Milestone order changed from “13” to “0”
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lightweight workflows for bioinformatics
john.mccallum (at plantandfood)
MF