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NP-Omix / BioCompass

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Error testing version 0.9.2 #49

Closed tiagolbiotech closed 7 years ago

tiagolbiotech commented 7 years ago

While running:

make INPUTDIR='/Users/Tiago/Desktop/BioCompass/antiSMASH_input' REFNAME='PAL' MULTIGENEBLASTDIR='/Users/Tiago/Desktop/BioCompass/multigeneblast' ALL

The following error occurred

mkdir -p `dirname /Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db`
export PATH="/Users/Tiago/anaconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/bin/EMBOSS-6.6.0/emboss:/usr/bin/standard-RAxML-master:/usr/bin/ncbi-blast-2.2.30+/bin:/usr/bin/MUMmer3.23/:/usr/local/bin/MEGAN:/usr/local/bin/diamond-0.7.10/bin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Users/Tiago/Desktop/BioCompass/multigeneblast"; \
        cd `dirname /Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db`; \
        python /Users/Tiago/Desktop/BioCompass/multigeneblast/makedb.py `basename /Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db` \
                `find /Users/Tiago/Desktop/BioCompass/outputs/database_clusters -name '*gbk' | awk '{print $0}' ORS=' '`
/bin/bash: /Users/Tiago/anaconda2/bin/python: Argument list too long
make[1]: *** [/Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db] Error 126
make: *** [ALL] Error 2
castelao commented 7 years ago

Delete database_clusters/MIBiG and try it again.

tiagolbiotech commented 7 years ago

It did not work deleting the MiBIG database, now the following error occur:

Error: all GenBank entries should start with 'LOCUS' identifier and contain a sequence after 'ORIGIN'. Exiting.
make[1]: *** [/Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db] Error 1
make: *** [ALL] Error 2

I believe it may have to do with the download script, which was working fine before for the same sample

castelao commented 7 years ago

Since it's working for me, I can't reproduce such error. I spent quite some time trying to figure out but it's not clear yet for me.

Try to use this modified version of the multigeneblast: https://bitbucket.org/castelao/multigeneblast/branch/dev

tiagolbiotech commented 7 years ago

It was probably related with the multigeneblast I had. I tried to used the branch dev but it didn't work. So I deleted the folder and dowloaded from sourceforge again and it worked.