Closed lucaspompeun closed 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?
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
I think you need to upgrade 3 things, in order of importance:
-qcov
options)[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
Updated the BLAST+ and it worked Thank you
Great news!
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
@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.
Yes this was fixed in 1.14.0 release. @lucaspompeun thank you for helping @Evan212 !
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
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
I get this:
channels:
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
That's good.
I often just do a full delete rm -fr $HOME/minoconda3
and start again too.
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:
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?
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!
UPDATE: ran prokka --setupdb
as recommended here and it worked! I think it was a combo of updating tools and resetting the databases.
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.
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
Hey, what's happening here?
Help! :)