Could not run command: cat prokka\/IS\.faa

lucaspompeun commented 5 years ago

Hey, what's happening here?

Could not run command: cat prokka\/IS.faa | parallel --gnu --plain -j 8 --block 88671 --recstart '>' --pipe blastp -query - -db /usr/local/prokka/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\/IS.blast 2> /dev/null

Help! :)

tseemann commented 5 years ago

I will need more information, ideally the whole screen log.

What does prokka --version say? What does which -a prokka say? What does prokka --setupdb do?

lucaspompeun commented 5 years ago

prokka --version: prokka 1.13.3
which -a prokka: /usr/bin/prokka

prokka --setupdb: 

> [13:40:05] Appending to PATH: /usr/local/prokka/bin/../binaries/linux
[13:40:05] Appending to PATH: /usr/local/prokka/bin/../binaries/linux/../common
[13:40:05] Appending to PATH: /usr/local/prokka/bin
[13:40:05] Cleaning databases in /usr/local/prokka/db
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Archaea/sprot.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/AMR.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/IS.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Bacteria/sprot.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Mitochondria/sprot.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/kingdom/Viruses/sprot.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Enterococcus.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Escherichia.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.phd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.phi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.phr
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.pin
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.pog
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.psd
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.psi
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/genus/Staphylococcus.psq
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/hmm/HAMAP.hmm.h3f
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/hmm/HAMAP.hmm.h3i
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/hmm/HAMAP.hmm.h3m
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/hmm/HAMAP.hmm.h3p
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Bacteria.i1f
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Bacteria.i1i
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Bacteria.i1m
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Bacteria.i1p
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Viruses.i1f
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Viruses.i1i
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Viruses.i1m
[13:40:05] Deleting unwanted file: /usr/local/prokka/db/cm/Viruses.i1p
[13:40:05] Cleaning complete.
[13:40:05] Looking for 'makeblastdb' - found /usr/bin/makeblastdb
[13:40:05] Determined makeblastdb version is 2.2
[13:40:05] Making kingdom BLASTP database: /usr/local/prokka/db/kingdom/Archaea/sprot
[13:40:05] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/prokka\/db\/kingdom\/Archaea\/sprot -logfile /dev/null
[13:40:05] Could not run command: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/prokka\/db\/kingdom\/Archaea\/sprot -logfile /dev/null

Log:

> [14:43:53] This is prokka 1.13.3
[14:43:53] Written by Torsten Seemann <torsten.seemann@gmail.com>
[14:43:53] Homepage is https://github.com/tseemann/prokka
[14:43:53] Local time is Tue Aug  6 14:43:53 2019
[14:43:53] You are lucas
[14:43:53] Operating system is linux
[14:43:53] You have BioPerl 1.007002
[14:43:53] System has 64 cores.
[14:43:53] Will use maximum of 8 cores.
[14:43:53] Annotating as >>> Bacteria <<<
[14:43:53] Generating locus_tag from 'ecoli_sspace/ecoli_sspace.final.scaffolds.
fasta' contents.
[14:43:53] Setting --locustag GJEAMHEE from MD5 03ea61eec365348cc787a8b2d337f828
[14:43:53] Creating new output folder: ecoli_prokka/
[14:43:53] Running: mkdir -p ecoli_prokka\/
[14:43:53] Using filename prefix: ecoli_.XXX
[14:43:53] Setting HMMER_NCPU=1
[14:43:53] Writing log to: ecoli_prokka//ecoli_.log
[14:43:53] Command: /usr/bin/prokka --outdir ecoli_prokka/ --prefix ecoli_ ecoli
_sspace/ecoli_sspace.final.scaffolds.fasta
[14:43:53] Appending to PATH: /usr/local/prokka/bin/../binaries/linux
[14:43:53] Appending to PATH: /usr/local/prokka/bin/../binaries/linux/../common
[14:43:53] Appending to PATH: /usr/local/prokka/bin
[14:43:53] Looking for 'aragorn' - found /usr/local/prokka/bin/../binaries/linux/aragorn
[14:43:53] Determined aragorn version is 1.2
[14:43:53] Looking for 'blastp' - found /usr/bin/blastp
[14:43:53] Determined blastp version is 2.2
[14:43:53] Looking for 'cmpress' - found /usr/bin/cmpress
[14:43:53] Determined cmpress version is 1.1
[14:43:53] Looking for 'cmscan' - found /usr/bin/cmscan
[14:43:53] Determined cmscan version is 1.1
[14:43:53] Looking for 'egrep' - found /bin/egrep
[14:43:53] Looking for 'find' - found /usr/bin/find
[14:43:53] Looking for 'grep' - found /bin/grep
[14:43:53] Looking for 'hmmpress' - found /usr/local/bin/hmmpress
[14:43:53] Determined hmmpress version is 3.2
[14:43:53] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
[14:43:53] Determined hmmscan version is 3.2
[14:43:53] Looking for 'java' - found /usr/bin/java
[14:43:53] Looking for 'less' - found /usr/bin/less
[14:43:53] Looking for 'makeblastdb' - found /usr/bin/makeblastdb
[14:43:53] Determined makeblastdb version is 2.2
[14:43:53] Looking for 'minced' - found /usr/local/prokka/bin/../binaries/linux/../common/minced
[14:43:53] Determined minced version is 2.0
[14:43:53] Looking for 'parallel' - found /usr/bin/parallel
[14:43:54] Determined parallel version is 20161222
[14:43:54] Looking for 'prodigal' - found /usr/local/bin/prodigal
[14:43:54] Determined prodigal version is 2.6
[14:43:54] Looking for 'prokka-genbank_to_fasta_db' - found /usr/local/prokka/bin/prokka-genbank_to_fasta_db
[14:43:54] Looking for 'sed' - found /bin/sed
[14:43:54] Looking for 'tbl2asn' - found /usr/local/prokka/bin/../binaries/linux/tbl2asn
[14:43:54] Determined tbl2asn version is 25.6
[14:43:54] Using genetic code table 11.
[14:43:54] Loading and checking input file: ecoli_sspace/ecoli_sspace.final.scaffolds.fasta
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold1|size296594
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold2|size244621
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold3|size201238
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold4|size168064
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold5|size167650
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold6|size138983
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold7|size129871
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold8|size128268
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold9|size105790
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold10|size105498
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold11|size105331
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold12|size103141
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold13|size102485
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold14|size95896
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold15|size94801
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold16|size93876
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold17|size93250
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold18|size91391
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold19|size91198
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold20|size90692
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold21|size73899
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold22|size70180
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold23|size68480
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold24|size64826
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold25|size63678
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold26|size61370
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold27|size60980
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold28|size60655
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold29|size59794
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold30|size58949
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold31|size58197
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold32|size57070
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold33|size54773
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold34|size52933
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold35|size52922
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold36|size52706
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold37|size52187
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold38|size50331
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold39|size48262
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold40|size46092
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold41|size44261
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold42|size41265
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold43|size39364
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold44|size34964
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold45|size32903
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold46|size32248
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold47|size31121
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold48|size29926
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold49|size27865
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold50|size26714
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold51|size25226
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold52|size23687
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold53|size21985
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold54|size21002
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold55|size20946
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold56|size20380
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold57|size20207
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold58|size18943
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold59|size18814
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold60|size18658
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold61|size17659
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold62|size16840
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold63|size16689
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold64|size15490
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold65|size15145
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold66|size14403
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold67|size14346
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold68|size13927
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold69|size12945
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold70|size12250
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold71|size12066
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold72|size12040
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold73|size11873
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold74|size11394
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold75|size10899
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold76|size10573
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold77|size10283
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold78|size8637
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold79|size8476
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold80|size7231
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold81|size6676
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold82|size6141
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold83|size6006
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold84|size5871
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold85|size5711
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold86|size5378
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold87|size5022
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold88|size5009
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold89|size4546
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold90|size4392
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold91|size4364
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold92|size4065
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold93|size3529
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold94|size3527
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold95|size3416
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold96|size3314
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold97|size3127
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold98|size2862
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold99|size2829
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold100|size2616
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold101|size2599
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold102|size2460
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold103|size2442
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold104|size2328
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold105|size2276
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold106|size2258
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold107|size2129
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold108|size2062
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold109|size1968
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold110|size1812
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold111|size1804
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold112|size1804
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold113|size1774
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold114|size1727
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold115|size1649
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold116|size1573
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold117|size1538
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold118|size1461
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold119|size1446
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold120|size1435
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold121|size1378
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold122|size1331
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold123|size1318
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold124|size1305
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold125|size1292
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold126|size1289
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold127|size1283
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold128|size1270
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold129|size1259
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold130|size1148
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold131|size1133
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold132|size1096
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold133|size1031
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold134|size972
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold135|size901
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold136|size872
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold137|size848
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold138|size800
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold139|size768
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold140|size761
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold141|size755
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold142|size741
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold143|size737
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold144|size734
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold145|size727
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold146|size716
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold147|size685
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold148|size658
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold149|size636
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold150|size622
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold151|size584
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold152|size541
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold153|size525
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold154|size481
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold155|size459
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold156|size458
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold157|size444
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold158|size418
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold159|size418
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold160|size417
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold161|size417
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold162|size399
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold163|size395
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold164|size393
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold165|size389
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold166|size380
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold167|size377
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold168|size367
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold169|size356
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold170|size326
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold171|size319
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold172|size304
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold173|size303
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold174|size301
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold175|size275
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold176|size268
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold177|size265
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold178|size265
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold179|size264
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold180|size262
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold181|size255
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold182|size254
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold183|size253
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold184|size251
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold185|size250
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold186|size250
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold187|size244
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold188|size239
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold189|size235
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold190|size217
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold191|size212
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold192|size209
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold193|size208
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold194|size200
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold195|size179
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold196|size165
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold197|size165
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold198|size163
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold199|size162
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold200|size162
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold201|size152
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold202|size142
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold203|size137
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold204|size133
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold205|size129
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold206|size129
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold207|size128
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold208|size128
[14:43:54] Changing illegal '|' to '_' in sequence name: scaffold209|size128
[14:43:54] Wrote 209 contigs totalling 4793428 bp.
[14:43:54] Predicting tRNAs and tmRNAs
[14:43:54] Running: aragorn -l -gc11  -w ecoli_prokka\/\/ecoli_\.fna
[14:43:57] 1 tRNA-Met c[52328,52403] 34 (cat)
[14:43:57] 2 tRNA-Phe c[171421,171496] 34 (gaa)
[14:43:57] 3 tRNA-Gly [282805,282878] 33 (ccc)
[14:43:57] 1 tRNA-Ser c[120849,120936] 35 (gga)
[14:43:57] 2 tRNA-Ser c[226589,226676] 35 (tga)
[14:43:57] 1 tRNA-Pro c[17361,17437] 35 (ggg)
[14:43:57] 1 tRNA-Ala c[19823,19898] 34 (ggc)
[14:43:57] 2 tRNA-Ala c[19938,20013] 34 (ggc)
[14:43:57] 3 tRNA-Val [22713,22788] 34 (tac)
[14:43:57] 4 tRNA-Val [22833,22908] 34 (tac)
[14:43:57] 5 tRNA-Val [22955,23030] 34 (tac)
[14:43:57] 6 tRNA-Lys [23035,23110] 34 (ttt)
[14:43:57] 1 tRNA-Asn [11106,11180] 33 (gtt)
[14:43:57] 1 tRNA-Phe c[59470,59545] 34 (gaa)
[14:43:57] 2 tRNA-Gly [88713,88788] 34 (gcc)
[14:43:57] 3 tRNA-Gly [88946,89021] 34 (gcc)
[14:43:57] 4 tRNA-Gly [89057,89132] 34 (gcc)
[14:43:57] 1 tRNA-Met c[44783,44859] 35 (cat)
[14:43:57] 2 tRNA-Met c[44893,44969] 35 (cat)
[14:43:57] 3 tRNA-Met c[45003,45079] 35 (cat)
[14:43:57] 1 tRNA-Leu c[54557,54643] 35 (cag)
[14:43:57] 2 tRNA-Leu c[54678,54764] 35 (cag)
[14:43:57] 3 tRNA-Leu c[54793,54879] 35 (cag)
[14:43:57] 1 tRNA-Leu [8368,8454] 35 (gag)
[14:43:57] 2 tRNA-Met [12237,12313] 35 (cat)
[14:43:57] 1 tRNA-Pro [53931,54007] 35 (cgg)
[14:43:57] 1 tRNA-Tyr c[65306,65390] 35 (gta)
[14:43:57] 2 tRNA-Tyr c[65600,65684] 35 (gta)
[14:43:57] 1 tRNA-Arg c[30979,31055] 35 (acg)
[14:43:57] 2 tRNA-Arg c[31254,31330] 35 (acg)
[14:43:57] 3 tRNA-Arg c[31393,31469] 35 (acg)
[14:43:57] 4 tRNA-Arg [31653,31724] 34 (tcg)
[14:43:57] 5 tRNA-Arg c[31668,31744] 35 (acg)
[14:43:57] 6 tRNA-Ser c[31748,31840] 35 (gct)
[14:43:57] 1 tRNA-Lys c[27580,27655] 34 (ttt)
[14:43:57] 2 tRNA-Lys c[27788,27863] 34 (ttt)
[14:43:57] 3 tRNA-Lys c[28010,28085] 34 (ttt)
[14:43:57] 4 tRNA-Val c[28089,28164] 34 (tac)
[14:43:57] 5 tRNA-Lys c[28314,28389] 34 (ttt)
[14:43:57] 6 tRNA-Val c[28392,28467] 34 (tac)
[14:43:57] 7 tRNA-Lys c[28503,28578] 34 (ttt)
[14:43:57] 1 tRNA-Ser [29212,29292] 38 (gga)
[14:43:57] 1 tRNA-Thr [61055,61130] 34 (cgt)
[14:43:57] 1 tRNA-Val [53304,53380] 35 (gac)
[14:43:57] 2 tRNA-Val [53385,53461] 35 (gac)
[14:43:57] 1 tmRNA [24837,25199] 90,125 ANDENYALAA**
[14:43:57] 1 tRNA-Pro c[16616,16692] 35 (tgg)
[14:43:57] 2 tRNA-Leu c[16735,16821] 35 (cag)
[14:43:57] 3 tRNA-His c[16842,16917] 34 (gtg)
[14:43:57] 4 tRNA-Arg c[16976,17052] 35 (ccg)
[14:43:57] 5 tRNA-Trp c[52397,52472] 34 (cca)
[14:43:57] 6 tRNA-Asp c[52481,52557] 35 (gtc)
[14:43:58] 1 tRNA-Met [31473,31549] 35 (cat)
[14:43:58] 2 tRNA-Leu [31559,31643] 35 (tag)
[14:43:58] 3 tRNA-Gln [31667,31741] 33 (ttg)
[14:43:58] 4 tRNA-Gln [31776,31850] 33 (ttg)
[14:43:58] 5 tRNA-Met [31866,31942] 35 (cat)
[14:43:58] 6 tRNA-Gln [31990,32064] 33 (ctg)
[14:43:58] 7 tRNA-Gln [32102,32176] 33 (ctg)
[14:43:58] 1 tRNA-Arg [4730,4806] 35 (tct)
[14:43:58] 1 tRNA-Leu c[5980,6064] 35 (caa)
[14:43:58] 1 tRNA-Asn c[10366,10441] 34 (gtt)
[14:43:58] 2 tRNA-Asn [12190,12265] 34 (gtt)
[14:43:58] 3 tRNA-Asn [14599,14674] 34 (gtt)
[14:43:58] 1 tRNA-Arg c[1503,1577] 34 (cct)
[14:43:58] 1 tRNA-SeC c[1474,1568] 35 (tca)
[14:43:58] 1 tRNA-Gly [9032,9107] 34 (gcc)
[14:43:58] 2 tRNA-Cys [9161,9234] 33 (gca)
[14:43:58] 3 tRNA-Leu [9247,9333] 35 (taa)
[14:43:58] 1 tRNA-Ser c[8987,9076] 35 (cga)
[14:43:58] 2 tRNA-Asn [10068,10143] 34 (gtt)
[14:43:58] 1 tRNA-Asp [50,126] 35 (gtc)
[14:43:58] 2 tRNA-Asp [8274,8350] 35 (gtc)
[14:43:58] 1 tRNA-Ser c[394,481] 35 (gga)
[14:43:58] 1 tRNA-Thr [134,209] 34 (ggt)
[14:43:58] 1 tRNA-Thr [3547,3622] 34 (tgt)
[14:43:58] 2 tRNA-Tyr [3631,3715] 35 (gta)
[14:43:58] 3 tRNA-Gly [3832,3906] 34 (tcc)
[14:43:58] 4 tRNA-Thr [3913,3988] 34 (ggt)
[14:43:58] 1 tRNA-Ala c[318,393] 34 (tgc)
[14:43:58] 2 tRNA-Ile c[436,512] 35 (gat)
[14:43:58] 1 tRNA-Glu [285,360] 35 (ttc)
[14:43:58] 1 tRNA-Glu c[251,326] 35 (ttc)
[14:43:58] 1 tRNA-Glu c[52,127] 35 (ttc)
[14:43:58] 1 tRNA-Ile [176,252] 35 (gat)
[14:43:58] 1 tRNA-Glu c[104,179] 35 (ttc)
[14:43:58] Found 86 tRNAs
[14:43:58] Predicting Ribosomal RNAs
[14:43:58] You need either Barrnap or RNAmmer installed to predict rRNAs!
[14:43:58] Skipping ncRNA search, enable with --rfam if desired.
[14:43:58] Total of 85 tRNA + rRNA features
[14:43:58] Searching for CRISPR repeats
[14:43:58] CRISPR1 scaffold9_size105790 88059 with 7 spacers
[14:43:58] CRISPR2 scaffold18_size91391 90898 with 6 spacers
[14:43:59] Found 2 CRISPRs
[14:43:59] Predicting coding sequences
[14:43:59] Contigs total 4793428 bp, so using single mode
[14:43:59] Running: prodigal -i ecoli_prokka\/\/ecoli_\.fna -c -m -g 11 -p single -f sco -q
[14:44:09] Excluding CDS which overlaps existing RNA (tRNA) at scaffold17_size93250:65127..65693 on + strand
[14:44:09] Excluding CDS which overlaps existing RNA (tRNA) at scaffold18_size91391:31118..31588 on + strand
[14:44:10] Excluding CDS which overlaps existing RNA (tRNA) at scaffold24_size64826:29282..29527 on + strand
[14:44:12] Found 4497 CDS
[14:44:12] Connecting features back to sequences
[14:44:12] Not using genus-specific database. Try --usegenus to enable it.
[14:44:12] Annotating CDS, please be patient.
[14:44:12] Will use 8 CPUs for similarity searching.
[14:44:14] There are still 4497 unannotated CDS left (started with 4497)
[14:44:14] Will use blast to search against /usr/local/prokka/db/kingdom/Bacteria/IS with 8 CPUs
[14:44:14] Running: cat ecoli_prokka\/\/IS\.faa | parallel --gnu --plain -j 8 --block 88665 --recstart '>' --pipe blastp -query - -db /usr/local/prokka/db/kingdom/Bacteria/IS -
evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > ecoli_prokka\/\/IS\.blast 2> /dev/null
[14:44:14] Could not run command: cat ecoli_prokka\/\/IS\.faa | parallel --gnu --plain -j 8 --block 88665 --recstart '>' --pipe blastp -query - -db /usr/local/prokka/db/kingdom
/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > ecoli_prokka\/\/IS\.blast 2> /dev/null

tseemann commented 5 years ago

I think you need to upgrade 3 things, in order of importance:

BLAST+ 2.7 or higher (you are on a very old 2.2 version which does not support -qcov options)
GNU Parallel (probably ok, but not 100% sure)
Prokka 1.13.7 (some bug fixes and newer databases)

[14:43:53] Looking for 'blastp' - found /usr/bin/blastp
[14:43:53] Determined blastp version is 2.2
[14:43:53] Looking for 'makeblastdb' - found /usr/bin/makeblastdb
[14:43:53] Determined makeblastdb version is 2.2
[14:43:53] Looking for 'parallel' - found /usr/bin/parallel
[14:43:54] Determined parallel version is 20161222

lucaspompeun commented 5 years ago

Updated the BLAST+ and it worked Thank you

tseemann commented 5 years ago

Great news!

Evan212 commented 5 years ago

Hello, I seem to have the same kind of problem. I have been trying to look around here for a solution but mainly it seems to be updating packages, but I am up to date I think. Thanks for the help!

(sorry for the spam I already posted on another channel but this one is more recent)

I updated the whole Prokka package so I'm guessing everything should be up-to-date)

Here is my full log: [11:33:34] This is prokka 1.14.0 [11:33:34] Written by Torsten Seemann torsten.seemann@gmail.com [11:33:34] Homepage is https://github.com/tseemann/prokka [11:33:34] Local time is Tue Aug 20 11:33:34 2019 [11:33:34] You are evan [11:33:34] Operating system is darwin [11:33:34] You have BioPerl 1.007002 [11:33:34] System has 2 cores. [11:33:34] Option --cpu asked for 8 cores, but system only has 2 [11:33:34] Will use maximum of 2 cores. [11:33:34] Annotating as >>> Bacteria <<< [11:33:34] Creating new output folder: AMR38_prokka [11:33:34] Running: mkdir -p AMR38_prokka [11:33:35] Using filename prefix: AMR38-prokka.XXX [11:33:35] Setting HMMER_NCPU=1 [11:33:35] Writing log to: AMR38_prokka/AMR38-prokka.log [11:33:35] Command: /Users/evan/miniconda3/bin/prokka --proteins CP027540 (D39V).gb --outdir AMR38_prokka --genus Streptococcus --species pneumoniae --strain AMR38 --locustag AMR38 --addgenes --prefix AMR38-prokka 11A-together-20190814.fasta [11:33:35] Appending to PATH: /Users/evan/miniconda3/bin [11:33:35] Looking for 'aragorn' - found /Users/evan/miniconda3/bin/aragorn [11:33:35] Determined aragorn version is 1.2 [11:33:35] Looking for 'barrnap' - found /Users/evan/miniconda3/bin/barrnap [11:33:35] Determined barrnap version is 0.9 [11:33:35] Looking for 'blastp' - found /Users/evan/miniconda3/bin/blastp [11:33:35] Determined blastp version is 2.9 [11:33:35] Looking for 'cmpress' - found /Users/evan/miniconda3/bin/cmpress [11:33:35] Determined cmpress version is 1.1 [11:33:35] Looking for 'cmscan' - found /Users/evan/miniconda3/bin/cmscan [11:33:35] Determined cmscan version is 1.1 [11:33:35] Looking for 'egrep' - found /usr/bin/egrep [11:33:35] Looking for 'find' - found /usr/bin/find [11:33:35] Looking for 'grep' - found /usr/bin/grep [11:33:35] Looking for 'hmmpress' - found /Users/evan/miniconda3/bin/hmmpress [11:33:35] Determined hmmpress version is 3.2 [11:33:35] Looking for 'hmmscan' - found /Users/evan/miniconda3/bin/hmmscan [11:33:35] Determined hmmscan version is 3.2 [11:33:35] Looking for 'java' - found /Users/evan/miniconda3/bin/java [11:33:35] Looking for 'less' - found /usr/bin/less [11:33:35] Looking for 'makeblastdb' - found /Users/evan/miniconda3/bin/makeblastdb [11:33:35] Determined makeblastdb version is 2.9 [11:33:35] Looking for 'minced' - found /Users/evan/miniconda3/bin/minced [11:33:36] Determined minced version is 4.0 [11:33:36] Looking for 'parallel' - found /Users/evan/miniconda3/bin/parallel [11:33:36] Determined parallel version is 20190722 [11:33:36] Looking for 'prodigal' - found /Users/evan/miniconda3/bin/prodigal [11:33:36] Determined prodigal version is 2.6 [11:33:36] Looking for 'prokka-genbank_to_fasta_db' - found /Users/evan/miniconda3/bin/prokka-genbank_to_fasta_db [11:33:36] Looking for 'sed' - found /usr/bin/sed [11:33:36] Looking for 'tbl2asn' - found /Users/evan/miniconda3/bin/tbl2asn [11:33:36] Determined tbl2asn version is 25.7 [11:33:36] Using genetic code table 11. [11:33:36] Loading and checking input file: 11A-together-20190814.fasta [11:33:36] Wrote 2 contigs totalling 2151859 bp. [11:33:36] Predicting tRNAs and tmRNAs [11:33:36] Running: aragorn -l -gc11 -w AMR38_prokka/AMR38-prokka.fna [11:33:37] 1 tRNA-Glu [28522,28593] 34 (ttc) [11:33:37] 2 tRNA-Ala [30441,30515] 35 (tgc) [11:33:37] 3 tRNA-Asn [33738,33811] 35 (gtt) [11:33:37] 4 tRNA-Tyr [827199,827279] 35 (gta) [11:33:37] 5 tRNA-Gln [827289,827360] 33 (ttg) [11:33:37] 6 tmRNA [841362,841706] 83,118 AKNNTSYALAA* [11:33:37] 7 tRNA-Ser c[841880,841970] 36 (gga) [11:33:37] 8 tRNA-Thr [974729,974801] 34 (ggt) [11:33:37] 9 tRNA-Arg c[1219846,1219919] 35 (ccg) [11:33:37] 10 tRNA-Arg c[1262831,1262902] 34 (cct) [11:33:37] 11 tRNA-Leu c[1525926,1526011] 35 (aag) [11:33:37] 12 tRNA-Lys [1694660,1694735] 35 (ctt) [11:33:37] 13 tRNA-Ser c[1801748,1801837] 36 (gct) [11:33:37] 14 tRNA-Ile c[1801842,1801917] 36 (gat) [11:33:37] 15 tRNA-Gly c[1801952,1802022] 33 (tcc) [11:33:37] 16 tRNA-Phe c[1802042,1802114] 34 (gaa) [11:33:37] 17 tRNA-Met c[1802118,1802191] 35 (cat) [11:33:37] 18 tRNA-Ser c[1802205,1802294] 37 (tga) [11:33:37] 19 tRNA-Met c[1802305,1802378] 35 (cat) [11:33:37] 20 tRNA-Met c[1802391,1802466] 36 (cat) [11:33:37] 21 tRNA-Pro c[1802470,1802545] 36 (tgg) [11:33:37] 22 tRNA-Arg c[1802560,1802633] 35 (acg) [11:33:37] 23 tRNA-Leu c[1802643,1802728] 35 (taa) [11:33:37] 24 tRNA-Gly c[1802736,1802807] 33 (gcc) [11:33:37] 25 tRNA-Thr c[1802830,1802902] 34 (tgt) [11:33:37] 26 tRNA-Leu c[1802920,1803003] 36 (tag) [11:33:37] 27 tRNA-Lys c[1803008,1803080] 34 (ttt) [11:33:37] 28 tRNA-Asp c[1803105,1803177] 34 (gtc) [11:33:37] 29 tRNA-Val c[1803180,1803252] 34 (tac) [11:33:37] 30 tRNA-Ala c[1806474,1806548] 35 (tgc) [11:33:37] 31 tRNA-Glu c[1808396,1808467] 34 (ttc) [11:33:37] 32 tRNA-Cys [1860604,1860677] 34 (gca) [11:33:37] 33 tRNA-Pro c[1898677,1898752] 36 (tgg) [11:33:37] 34 tRNA-Arg c[1898767,1898840] 35 (acg) [11:33:37] 35 tRNA-Leu c[1898850,1898935] 35 (taa) [11:33:37] 36 tRNA-Gly c[1898943,1899014] 33 (gcc) [11:33:37] 37 tRNA-Thr c[1899037,1899109] 34 (tgt) [11:33:37] 38 tRNA-Leu c[1899127,1899210] 36 (tag) [11:33:37] 39 tRNA-Lys c[1899215,1899287] 34 (ttt) [11:33:37] 40 tRNA-Asp c[1899312,1899384] 34 (gtc) [11:33:37] 41 tRNA-Val c[1899387,1899459] 34 (tac) [11:33:37] 42 tRNA-Ala c[1902681,1902755] 35 (tgc) [11:33:37] 43 tRNA-Glu c[1904603,1904674] 34 (ttc) [11:33:37] 44 tRNA-Leu c[1960329,1960414] 36 (caa) [11:33:37] 45 tRNA-Gln c[1960422,1960495] 34 (ttg) [11:33:37] 46 tRNA-His c[1960504,1960578] 35 (gtg) [11:33:37] 47 tRNA-Trp c[1960591,1960663] 34 (cca) [11:33:37] 48 tRNA-Tyr c[1960666,1960748] 36 (gta) [11:33:37] 49 tRNA-Phe c[1960760,1960832] 34 (gaa) [11:33:37] 50 tRNA-Met c[1960836,1960909] 35 (cat) [11:33:37] 51 tRNA-Ser c[1960923,1961012] 37 (tga) [11:33:37] 52 tRNA-Ile c[1961094,1961169] 36 (gat) [11:33:37] 53 tRNA-Gly c[1961203,1961275] 34 (tcc) [11:33:37] 54 tRNA-Val c[1961280,1961352] 34 (tac) [11:33:37] 55 tRNA-Ala c[1964574,1964648] 35 (tgc) [11:33:37] 56 tRNA-Glu c[1966496,1966567] 34 (ttc) [11:33:37] 1 tRNA-Asn c[23911,23984] 35 (gtt) [11:33:37] 2 tRNA-Glu c[23990,24061] 34 (ttc) [11:33:37] 3 tRNA-Arg c[26498,26571] 35 (tct) [11:33:37] Found 59 tRNAs [11:33:37] Predicting Ribosomal RNAs [11:33:37] Running Barrnap with 2 threads [11:33:40] 1 11A-start 28848 16S ribosomal RNA [11:33:40] 2 11A-start 30641 23S ribosomal RNA [11:33:40] 3 11A-start 33620 5S ribosomal RNA [11:33:40] 4 11A-start 1803261 5S ribosomal RNA [11:33:40] 5 11A-start 1803452 23S ribosomal RNA [11:33:40] 6 11A-start 1806600 16S ribosomal RNA [11:33:40] 7 11A-start 1899468 5S ribosomal RNA [11:33:40] 8 11A-start 1899659 23S ribosomal RNA [11:33:40] 9 11A-start 1902807 16S ribosomal RNA [11:33:40] 10 11A-start 1961361 5S ribosomal RNA [11:33:40] 11 11A-start 1961552 23S ribosomal RNA [11:33:40] 12 11A-start 1964700 16S ribosomal RNA [11:33:40] Found 12 rRNAs [11:33:40] Skipping ncRNA search, enable with --rfam if desired. [11:33:40] Total of 70 tRNA + rRNA features [11:33:40] Searching for CRISPR repeats [11:33:40] Found 0 CRISPRs [11:33:40] Predicting coding sequences [11:33:40] Contigs total 2151859 bp, so using single mode [11:33:40] Running: prodigal -i AMR38_prokka/AMR38-prokka.fna -c -m -g 11 -p single -f sco -q [11:33:48] Found 2165 CDS [11:33:48] Connecting features back to sequences [11:33:48] Not using genus-specific database. Try --usegenus to enable it. [11:33:48] Preparing user-supplied primary BLAST annotation source: CP027540 (D39V).gb [11:33:48] Guessed source was in genbank format. [11:33:48] Converting genbank 'CP027540 (D39V).gb' into Prokka FASTA 'AMR38_prokka/proteins.faa' [11:33:48] Running: prokka-genbank_to_fasta_db --format genbank CP027540\ (D39V).gb > AMR38_prokka/proteins.faa 2> /dev/null [11:33:51] Running: makeblastdb -dbtype prot -in AMR38_prokka/proteins.faa -out AMR38_prokka/proteins -logfile /dev/null [11:33:52] Using /inference source as 'CP027540 (D39V).gb' [11:33:52] Annotating CDS, please be patient. [11:33:52] Will use 2 CPUs for similarity searching. [11:33:52] There are still 2165 unannotated CDS left (started with 2165) [11:33:52] Will use blast to search against AMR38_prokka/proteins with 2 CPUs [11:33:52] Running: cat AMR38_prokka/proteins.faa | parallel --gnu --plain -j 2 --block 156417 --recstart '>' --pipe blastp -query - -db AMR38_prokka/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > AMR38_prokka/proteins.blast 2> /dev/null [11:33:53] Could not run command: cat AMR38_prokka/proteins.faa | parallel --gnu --plain -j 2 --block 156417 --recstart '>' --pipe blastp -query - -db AMR38_prokka/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > AMR38_prokka/proteins.blast 2> /dev/null

lucaspompeun commented 5 years ago

@Evan212 It's just update the blast+. Just that! You should download the executables files here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ And than, it's just add the executables folder (bin) to the Linux Path. The newest version on this link is 2.9, the used version on Prokka.

tseemann commented 5 years ago

Yes this was fixed in 1.14.0 release. @lucaspompeun thank you for helping @Evan212 !

Evan212 commented 5 years ago

I'm on macOS. And I think it should be the latest version no? I downloaded from your link but it does not change the result. Sorry if I do anything wrong, thank you for helping me!

Edit: I have blast 2.9 and prokka 1.14

tseemann commented 5 years ago

Github does not include all the dependences. Well, i do bundle some things, but they are not guaranteed to work. You should use either conda or brew to install. On Mac, homebrew is probably the easiest. Follow instructions at http://brew.sh then brew install brewsci/bio/prokka ?

UPDATE: oh i see you are using conda. not sure what is going on. what does cat $HOME/.condarc say?

You want this order:

channels:
  - conda-forge
  - bioconda
  - defaults

Evan212 commented 5 years ago

I get this:

channels:

conda-forge
bioconda
default
defaults

I managed to solve my problem by running the exact same thing on my university cluster, so not sure what was wrong with my computer

tseemann commented 5 years ago

That's good. I often just do a full delete rm -fr $HOME/minoconda3 and start again too.

Betty-624 commented 4 years ago

I met the same problem. this is the log: PROKKA.log my prokka version is 1.14, and blast version is 2.9. And configuration is channels:

conda-forge
bioconda
defaults. what else that I can do to correct that? Thanks for your helping!

phiweger commented 3 years ago

Problem persists for

Could not run command: cat prokka\/target\.IS\.tmp\.8\.faa | parallel --gnu --plain -j 8 --block 100543 --recstart '>' --pipe blastp -query - -db /opt/conda/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\/target\.IS\.tmp\.8\.blast 2> /dev/null

blastp -version
# 2.10.1
prokka --version
# 1.14.6

Both installed using conda. @tseemann could this be a problem w/ blastp being too recent?

sevance commented 3 years ago

Hi all - I am having the same issues as above trying to run prokka with the most updated version. I am running this from our university's cluster in a conda environment (all tools are within miniconda3/envs/prokka/bin/)

prokka 1.14.6 blastp: 2.9.0+ GNU parallel 20210622

shortened output with error included:

[21:45:21] Deleting unwanted file: PROKKA_07212021/PROKKA_07212021.AMR.tmp.39543.faa
[21:45:21] Deleting unwanted file: PROKKA_07212021/PROKKA_07212021.AMR.tmp.39543.blast
[21:45:22] There are still 2148 unannotated CDS left (started with 2148)
[21:45:22] Will use blast to search against /oak/stanford/scg/lab_asbhatt/sevance/tools/miniconda3/envs/prokka/db/kingdom/Bacteria/sprot with 8 CPUs
[21:45:22] Running: cat PROKKA_07212021\/PROKKA_07212021\.sprot\.tmp\.39543\.faa | parallel --gnu --plain -j 8 --block 41424 --recstart '>' --pipe blastp -query - -db /oak/stanford/scg/lab_asbhatt/sevance/tools/miniconda3/envs/prokka/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_07212021\/PROKKA_07212021\.sprot\.tmp\.39543\.blast 2> /dev/null
[21:45:30] Could not run command: cat PROKKA_07212021\/PROKKA_07212021\.sprot\.tmp\.39543\.faa | parallel --gnu --plain -j 8 --block 41424 --recstart '>' --pipe blastp -query - -db /oak/stanford/scg/lab_asbhatt/sevance/tools/miniconda3/envs/prokka/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_07212021\/PROKKA_07212021\.sprot\.tmp\.39543\.blast 2> /dev/null

Any help would be really appreciated!

sevance commented 3 years ago

UPDATE: ran prokka --setupdb as recommended here and it worked! I think it was a combo of updating tools and resetting the databases.

ShailNair commented 1 year ago

For those encountering the error even after updating dependencies, Prokka, and resetting the database, you can try re-running the failed command without the 2> /dev/null and you will find out the exact error. In my case, the tmp directory was not found as I had modified the tmp directory path. Resetting the tmp directory path solved the problem.

2> /dev/null ## redirects the error output to /dev/null, discarding any error messages. 
Re-running the failed command without 2> /dev/null will display the error.

Sya-98 commented 9 months ago

I cannot run prokka, whenever I run, it said I need to run setup and the file for the prokka not found. Can anybody help

tseemann / prokka

Could not run command: cat prokka\/IS\.faa #402