Moamoa Moa → v1.1

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]$