#31 new
john.mccallum (at plantandfood)

Warn when a template is outdated

Reported by john.mccallum (at plantandfood) | May 30th, 2011 @ 11:02 PM | in v1.1

the process CL works fine...but

[cfljam@pgenome 40.assemble]$ source ~/.bashrc [cfljam@pgenome 40.assemble]$ moa run Warning: Removing a stale lockfile
Error: no in or output files
[cfljam@pgenome 40.assemble]$ moa clean [cfljam@pgenome 40.assemble]$ pwd /data/moa/onion/20.genomic.sequencing/40.assemble [cfljam@pgenome 40.assemble]$ moa clean [cfljam@pgenome 40.assemble]$ moa show postcommand L awk '$2=="Singleton" {print $1}' DHSkim/454ReadStatus.txt > singletons.lst;sed 's/contig/CUDH2122_/' DHSkim/454AllContigs.fna > CUDH2122_contigs.fasta
precommand o (undefined)
process L runAssembly -force -o DHSkim -a 100 -minlen 45 -tr -rip ../00.raw/MID6.sff
project L DHskim
title L Newbler assembly of reads
[cfljam@pgenome 40.assemble]$ moa run Error: no in or output files
[cfljam@pgenome 40.assemble]$

Comments and changes to this ticket

  • MF

    MF May 31st, 2011 @ 01:47 AM

    • State changed from “new” to “open”

    Think I fixed it

  • MF

    MF May 31st, 2011 @ 09:03 PM

    • State changed from “open” to “resolved”

    Seems to work now..

  • john.mccallum (at plantandfood)

    john.mccallum (at plantandfood) May 31st, 2011 @ 11:07 PM

    • State changed from “resolved” to “new”

    Not fixed I think

    {also how about re-ordering the show command so postcommand is after process?}

    [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ pwd /data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ source ~/.bashrc [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ moa show postcommand L awk '/ssaha:SNP/ {print $2, "ssaha2SNP","SNP",$9,$9, "1",".",".","ID=$2 }' ssaha2SNP.out > ssaha2SNP.gff [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$

  • MF

    MF June 1st, 2011 @ 04:22 AM

    • Tag changed from “simple” to “template refresh”

    It is resolved - You need to run moa refresh - the template code was still old - so that needs updating...

    (a downside to keeping template code in your directory) - I'll change this ticket to providing a warning if your template is outdated..

  • MF

    MF June 1st, 2011 @ 04:23 AM

    • Title changed from “Simple template bug?” to “Warn when a template is outdated”
  • john.mccallum (at plantandfood)

    john.mccallum (at plantandfood) June 1st, 2011 @ 04:26 AM

    Still wonky...is this permission defaults??

    [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ pwd /data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ ls -l .. total 60
    drwxrwxr-x 4 cflmwf users 4096 Jun 1 10:36 00.Candidates
    drwxrwxr-x 3 cflmwf users 4096 May 11 11:12 01.Candidate_BLASTdb
    drwxrwxr-x 5 cflmwf users 4096 May 4 13:31 05.TBLASTN_DH2150
    drwxrwxr-x 5 cflmwf users 4096 Jun 1 09:47 06.TBLASTN_USDA
    drwxrwxr-x 5 cflmwf users 4096 May 11 12:54 07.BLASTX_DH2150
    drwxrwxr-x 5 cfljam users 4096 Jun 1 10:27 08.TBLASTN_USDA_5225
    drwxrwxr-x 5 cfljam users 4096 Jun 1 10:22 09.TBLASTN_USDA_OH1
    drwxrwxr-x 4 cflmwf users 4096 May 11 12:47 10.gsMapper_Nasik
    drwxrwxr-x 4 cflmwf users 4096 May 11 12:15 11.gsMapper_NasikToUSDACGs
    drwxrwxr-x 4 cflmwf users 4096 May 11 12:26 12.gsMapper_DH2150ToUSDACGs
    drwxrwxr-x 3 cflmwf users 4096 May 4 10:06 20.primersearch
    drwxrwxr-x 3 cflmwf users 4096 May 11 13:35 21.USDA_CG_primersearch
    drwxrwxr-x 3 cflmwf users 4096 May 4 14:16 30.primerDesign
    drwxrwxr-x 3 cflmwf users 4096 May 5 09:05 35.primersearchSQL
    drwxrwxr-x 3 cfljam users 4096 Jun 1 11:05 40.OH1onto5225_ssahaSNP
    [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$ moa refresh Warning: Encountered a run error?
    Traceback (most recent call last):
    File "/opt/moa10/bin/moa", line 318, in

    run_1()

    File "/opt/moa10/bin/moa", line 292, in run_1

    run_2()

    File "/opt/moa10/bin/moa", line 246, in run_2

    run_3(wd)

    File "/opt/moa10/bin/moa", line 191, in run_3

    pluginHandler.runCallback(job, command)

    File "/opt/moa10/lib/python/moa/plugin/init.py", line 85, in runCallback

    commandInfo['call'](job)

    File "/opt/moa10/lib/python/moa/plugin/template.py", line 73, in refresh

    job.refreshTemplate()

    File "/opt/moa10/lib/python/moa/job.py", line 310, in refreshTemplate

    moa.template.refresh(self.wd)

    File "/opt/moa10/lib/python/moa/template/init.py", line 114, in refresh

    provider=meta.get('provider', None))

    File "/opt/moa10/lib/python/moa/template/init.py", line 57, in installTemplate

    PROVIDERS.installTemplate(wd, tName, provider)

    File "/opt/moa10/lib/python/moa/template/provider/init.py", line 101, in installTemplate

    p.installTemplate(wd, tName)

    File "/opt/moa10/lib/python/moa/template/provider/core.py", line 67, in installTemplate

    shutil.rmtree(extraFileDir)

    File "/usr/lib64/python2.6/shutil.py", line 221, in rmtree

    onerror(os.remove, fullname, sys.exc_info())

    File "/usr/lib64/python2.6/shutil.py", line 219, in rmtree

    os.remove(fullname)

    OSError: [Errno 13] Permission denied: '/data/moa/onion/70.CG_marker_design/30.Flowering/40.OH1onto5225_ssahaSNP/.moa/template.d/meta'
    [cfljam@pgenome 40.OH1onto5225_ssahaSNP]$

  • MF

    MF June 1st, 2011 @ 05:51 AM

    Yes - it is - sorry about that - i've asked ray to set them a little
    less restrictive - now every time you do something you automatically
    deny everybody else the right to edit it, possibly even look at it..

    I've restored the permissions..

    cheers
    Mark

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