This needs -f force flag added (simple) or a clean method
[cfljam@pgenome 93.gsmapper_TSA_submit]$ moa show gsmap_name L
Map_Nasik_to_SNP_markers_DHrefV2
jobid L gsMapper_CUDH2150TSA
name L test
postcommand L /opt/galaxy_pfr_tools/PCR_markers/gsmapper2gff.sh
out/454AllDiffs.txt > CUDH2150_TSA_AllDiffs.gff;
/opt/galaxy_pfr_tools/PCR_markers/gsmapper2gff.sh
out/454HCDiffs.txt CUDH2150_TSA_HCDiffs.gff
precommand L cat
/data/moa/db/onion/12.CUDHLF_TSA/CUDH2150_TSA.fasta
../96.Singletons/20.submit/clean_singletons.fasta |sed
's/(>\w)\s.*/\1/' > reference.fasta
reference_fasta L reference.fasta
sfffile L ../00.raw/Nasik_GLX_reads.sff
title L Map Nasik Red to CUDH2150 TSA Final
[cfljam@pgenome 93.gsmapper_TSA_submit]$ moa clean ERROR!
Unexpected error
Moa: Error running clean
Moa:Warning: Encountered a run error?
Traceback (most recent call last):
File "/opt/moa10/bin/moa", line 378, in
run_1()
File "/opt/moa10/bin/moa", line 338, in run_1
run_2()
File "/opt/moa10/bin/moa", line 288, in run_2
run_3(wd)
File "/opt/moa10/bin/moa", line 236, in run_3
job.simpleExecute(command)
File "/opt/moa10/lib/python/moa/job.py", line 226, in
simpleExecute
return self.backend.simpleExecute(commandList)
File
"/opt/moa10/lib/python/moa/backend/gnumake/init.py",
line 47, in simpleExecute
self.execute(command)
File
"/opt/moa10/lib/python/moa/backend/gnumake/init.py",
line 80, in execute
self.job.makeArgs.append('-s')
AttributeError: 'Job' object has no attribute 'makeArgs'
[cfljam@pgenome 93.gsmapper_TSA_submit]$ moa run make:
No rule to make target prepare'. Stop.
Moa:Warning: Removing a stale lockfile
/opt/moa10/lib/gnumake/plugins/adhoc.mk:27: warning: overriding
commands for targetmoa_plugin_adhoc_test'
/opt/moa10/lib/gnumake/plugins/adhoc.mk:27: warning: ignoring old
commands for target moa_plugin_adhoc_test'
/opt/moa10/lib/gnumake/plugins/info.mk:36: warning: overriding
commands for targetinfo_header'
/opt/moa10/lib/gnumake/plugins/info.mk:36: warning: ignoring old
commands for target info_header'
/opt/moa10/lib/gnumake/plugins/info.mk:79: warning: overriding
commands for targetmoa_plugin_info_test'
/opt/moa10/lib/gnumake/plugins/info.mk:79: warning: ignoring old
commands for target moa_plugin_info_test'
/opt/moa10/lib/gnumake/__core.mk:77: warning: overriding commands
for targetmoa_finished'
/opt/moa10/lib/gnumake/core.mk:77: warning: ignoring old
commands for target moa_finished'
/opt/moa10/lib/gnumake/__core.mk:84: warning: overriding commands
for targetmoa_main_target'
/opt/moa10/lib/gnumake/core.mk:84: warning: ignoring old
commands for target moa_main_target'
.moa/template.d/gsMapper.mk:40: warning: overriding commands for
targetout.gff' .moa/template.d/gsMapper.mk:40: warning:
ignoring old commands for target out.gff'
.moa/template.d/gsMapper.mk:78: warning: overriding commands for
targetimproved.HCDiffs' .moa/template.d/gsMapper.mk:78:
warning: ignoring old commands for target improved.HCDiffs'
.moa/template.d/gsMapper.mk:81: warning: overriding commands for
targetreads.index' .moa/template.d/gsMapper.mk:81: warning:
ignoring old commands for target reads.index'
.moa/template.d/gsMapper.mk:94: warning: overriding commands for
targetout/454HCDiffs.txt' .moa/template.d/gsMapper.mk:94:
warning: ignoring old commands for target out/454HCDiffs.txt'
.moa/template.d/gsMapper.mk:102: warning: overriding commands for
targetgsMapper_clean' .moa/template.d/gsMapper.mk:102:
warning: ignoring old commands for target `gsMapper_clean' Error:
Project directory already exists: out.
Use "-force" option to force its resetting. Error in runMapping:
Error while creating the mapping project.
make: [out/454HCDiffs.txt] Error 255
Moa: Error running run (1 sec)
[cfljam@pgenome 93.gsmapper_TSA_submit]$
milberalinas