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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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error while running Prokka #627

Open shashank-KU opened 2 years ago

shashank-KU commented 2 years ago

I am getting an error while running PROKKA-

[13:12:05] There are still 2808 unannotated CDS left (started with 2808)
[13:12:05] Will use blast to search against /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS with 6 CPUs
[13:12:05] Running: cat prokka_GCA_000008285\/PROKKA_04082022\.IS\.tmp\.32109\.faa | parallel --gnu --plain -j 6 --block 73260 --recstart '>' --pipe blastp -query - -db /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka_GCA_000008285\/PROKKA_04082022\.IS\.tmp\.32109\.blast 2> /dev/null
[13:12:27] Could not run command: cat prokka_GCA_000008285\/PROKKA_04082022\.IS\.tmp\.32109\.faa | parallel --gnu --plain -j 6 --block 73260 --recstart '>' --pipe blastp -query - -db /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka_GCA_000008285\/PROKKA_04082022\.IS\.tmp\.32109\.blast 2> /dev/nul

here are the details-

prokka --version
prokka 1.14.6
which -a prokka
~/miniconda3/envs/metawrap-env/bin/prokka
parallel --version
GNU parallel 20210822
prokka --setupdb
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
[13:20:23] Appending to PATH: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/bin
[13:20:23] Cleaning databases in /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot.pto
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR.pto
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS.pto
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot.pto
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot.pto
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.pdb
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.phd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.phi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.phr
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.pin
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.pog
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.pot
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.psd
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.psi
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.psq
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.ptf
[13:20:23] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot.pto
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.pdb
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.phd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.phi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.phr
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.pin
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.pog
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.pot
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.psd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.psi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.psq
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.ptf
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus.pto
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.pdb
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.phd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.phi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.phr
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.pin
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.pog
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.pot
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.psd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.psi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.psq
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.ptf
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia.pto
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.pdb
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.phd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.phi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.phr
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.pin
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.pog
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.pot
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.psd
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.psi
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.psq
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.ptf
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus.pto
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3f
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3i
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3m
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3p
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1f
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1i
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1m
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1p
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1f
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1i
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1m
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1p
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1f
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1i
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1m
[13:20:24] Deleting unwanted file: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1p
[13:20:24] Cleaning complete.
[13:20:24] Looking for 'makeblastdb' - found /mnt/users/shgu/miniconda3/envs/metawrap-env/bin/makeblastdb
[13:20:25] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
[13:20:25] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Archaea/sprot
[13:20:25] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Archaea\/sprot -logfile /dev/null
[13:20:25] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/sprot
[13:20:25] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Bacteria\/sprot -logfile /dev/null
[13:20:27] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Mitochondria/sprot
[13:20:27] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Mitochondria\/sprot -logfile /dev/null
[13:20:28] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Viruses/sprot
[13:20:28] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Viruses\/sprot -logfile /dev/null
[13:20:28] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/IS
[13:20:28] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Bacteria\/IS -logfile /dev/null
[13:20:29] Making kingdom BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/kingdom/Bacteria/AMR
[13:20:29] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/kingdom\/Bacteria\/AMR -logfile /dev/null
[13:20:29] Making genus BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Enterococcus
[13:20:29] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/genus\/Enterococcus -logfile /dev/null
[13:20:30] Making genus BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Escherichia
[13:20:30] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/genus\/Escherichia -logfile /dev/null
[13:20:30] Making genus BLASTP database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/genus/Staphylococcus
[13:20:30] Running: makeblastdb -hash_index -dbtype prot -in \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/genus\/Staphylococcus -logfile /dev/null
[13:20:31] Looking for 'hmmpress' - found /mnt/users/shgu/miniconda3/envs/metawrap-env/bin/hmmpress
[13:20:31] Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
[13:20:31] Pressing HMM database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm
[13:20:31] Running: hmmpress \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/hmm\/HAMAP\.hmm
Working...    done.
Pressed and indexed 1536 HMMs (1536 names).
Models pressed into binary file:   /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3m
SSI index for binary model file:   /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3i
Profiles (MSV part) pressed into:  /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3f
Profiles (remainder) pressed into: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/hmm/HAMAP.hmm.h3p
[13:20:33] Looking for 'cmpress' - found /mnt/users/shgu/miniconda3/envs/metawrap-env/bin/cmpress
[13:20:33] Determined cmpress version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
[13:20:33] Pressing CM database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses
[13:20:33] Running: cmpress \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/cm\/Viruses
Working...    done.
Pressed and indexed 239 CMs and p7 HMM filters (239 names and 239 accessions).
Covariance models and p7 filters pressed into binary file:  /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1m
SSI index for binary covariance model file:                 /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1f
Optimized p7 filter profiles (remainder) pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Viruses.i1p
[13:20:34] Pressing CM database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria
[13:20:34] Running: cmpress \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/cm\/Bacteria
Working...    done.
Pressed and indexed 1127 CMs and p7 HMM filters (1127 names and 1127 accessions).
Covariance models and p7 filters pressed into binary file:  /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1m
SSI index for binary covariance model file:                 /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1f
Optimized p7 filter profiles (remainder) pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Bacteria.i1p
[13:20:35] Pressing CM database: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea
[13:20:35] Running: cmpress \/net\/fs\-1\/home01\/shgu\/miniconda3\/envs\/metawrap\-env\/db\/cm\/Archaea
Working...    done.
Pressed and indexed 152 CMs and p7 HMM filters (152 names and 152 accessions).
Covariance models and p7 filters pressed into binary file:  /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1m
SSI index for binary covariance model file:                 /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1f
Optimized p7 filter profiles (remainder) pressed into:      /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db/cm/Archaea.i1p
[13:20:35] Looking for databases in: /net/fs-1/home01/shgu/miniconda3/envs/metawrap-env/db
[13:20:35] * Kingdoms: Archaea Bacteria Mitochondria Viruses
[13:20:35] * Genera: Enterococcus Escherichia Staphylococcus
[13:20:35] * HMMs: HAMAP
[13:20:35] * CMs: Archaea Bacteria Viruses

Any suggestions?

ne1al commented 2 years ago

@shashank-KU Did you figure out why? @tseemann prokka was running fine then suddenly I had this error explained here, any advice?