search

NP-Omix / BioCompass

Other
5 stars 3 forks source link

Bug creating multigeneblast database at version 0.9.1 #47

Closed tiagolbiotech closed 7 years ago

tiagolbiotech commented 7 years ago

After reinstalling BioCompass, while running the command:

make INPUTDIR='/Users/Tiago/Desktop/BioCompass/antiSMASH_input' REFNAME='PAL' MULTIGENEBLASTDIR='/Users/Tiago/Desktop/BioCompass/multigeneblast' TESTING=1 ALL

The following error happen:

mkdir -p `dirname /Users/Tiago/Desktop/BioCompass/outputs/tables/PAL_db`
export PATH="/Users/Tiago/anaconda2/bin:/Users/Tiago/anaconda2/bin:/Users/Tiago/anaconda/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/bin/multigeneblast_1.1.13:/usr/sbin:/sbin:/usr/bin/EMBOSS-6.6.0/emboss:/usr/bin/standard-RAxML-master:/usr/bin/ncbi-blast-2.2.30+/bin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/usr/local/mysql/bin:/usr/local/bin/MEGAN:/Users/Tiago/Desktop/Gene_Cluster_Network/multigeneblast:/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=' '`
Creating FASTA file
Checking files for suitability: ACEB01000004_100368-99975.gbk, ACNO01000004_325040-347697.gbk, ACSH02000002_308689-352815.gbk, ADNW02000013_111712-196253.gbk, [...]
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