Question: Abyss-map complains 'missing arguments'
gravatar for RoseString
2.6 years ago by
RoseString10 wrote:

I am running the latest Abyss 2.0.2. My command line is:

abyss-pe np=16 name=SWS k=70 lib='pe' mp='mp1 mp2 mp3 mp4' \
se='SWS_SE.trimmomatic.fq.gz' \
pe='SWS_PE_1.trimmomatic.fq.gz SWS_PE_2.trimmomatic.fq.gz' \
mp1='SWS_MP_1-4Kb_1.trimmomatic.fq.gz SWS_MP_1-4Kb_2.trimmomatic.fq.gz' \
mp2='SWS_MP_4-7Kb_1.trimmomatic.fq.gz SWS_MP_4-7Kb_2.trimmomatic.fq.gz' \
mp3='SWS_MP_7-10Kb_1.trimmomatic.fq.gz SWS_MP_7-10Kb_2.trimmomatic.fq.gz' \
mp4='SWS_MP_10-15Kb_1.trimmomatic.fq.gz SWS_MP_10-15Kb_2.trimmomatic.fq.gz'

Everything was ok until abyss got to the abyss-map step, it complained 'abyss-map: missing arguments'. The missing argument seems to be SWS_PE_1.trimmomatic.fq.gz-3.hist based on the error message. I checked the folder, and this file is indeed not there. Any ideas? The full log can be seen here.

Thank you in advance!

abyss • 793 views
ADD COMMENTlink modified 2.6 years ago by benv710 • written 2.6 years ago by RoseString10

Actually it's the command abyss-map -j16 -l40 SWS-3.fa that complains 'missing argument'. I checked abyss-map --help, and abyss-map [OPTION]... QUERY... TARGET needs both query and target, but the command generated by abyss only has one argument?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by RoseString10
gravatar for benv
2.6 years ago by
benv710 wrote:

This type of error (abyss-map missing arguments), is usually caused by a problem with how the input files are specified.

In this case, abyss-pe is having trouble because pe is a reserved variable, but you are using it like a user-defined variable. You could fix the problem by changing lib='pe' => pe='my_pe' and pe='...' to my_pe='...'. (For example.)

ADD COMMENTlink written 2.6 years ago by benv710

It works! Thank you!

ADD REPLYlink written 2.6 years ago by RoseString10
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