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”
Please Sign in or create a free account to add a new ticket.
With your very own profile, you can contribute to projects, track your activity, watch tickets, receive and update tickets through your email and much more.
Create new ticket
Create your profile
Help contribute to this project by taking a few moments to create your personal profile. Create your profile ยป
lightweight workflows for bioinformatics
john.mccallum (at plantandfood)
MF