Question: Abyss-map complains 'missing arguments'
gravatar for RoseString
23 months ago by
RoseString0 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 • 648 views
ADD COMMENTlink modified 23 months ago by benv710 • written 23 months ago by RoseString0

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 23 months ago • written 23 months ago by RoseString0
gravatar for benv
23 months 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 23 months ago by benv710

It works! Thank you!

ADD REPLYlink written 23 months ago by RoseString0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1972 users visited in the last hour