Prokka error

[amardeepranu]

Getting an error on the following step, any help would be appreciated!

[66/af4c33] process > GAP:PROCESS_SINGLETON_GENOMES:PROKKA (MGYG000000010)  [ 42%] 3 of 7, failed: 1

Error:

ERROR ~ Error executing process > 'GAP:PROCESS_SINGLETON_GENOMES:PROKKA (MGYG000000030)'

Caused by:
  Process `GAP:PROCESS_SINGLETON_GENOMES:PROKKA (MGYG000000030)` terminated with an error exit status (2)

Command executed:

  cat MGYG000000030.fa | tr '-' ' ' > MGYG000000030_cleaned.fasta
  
  export JAVA_TOOL_OPTIONS="-XX:-UsePerfData"
  
  prokka MGYG000000030_cleaned.fasta     --cpus 8     --kingdom 'Bacteria'     --outdir MGYG000000030_prokka     --prefix MGYG000000030     --force     --locustag MGYG000000030

Command exit status:
  2

Command output:
  (empty)

Command error:
  [18:57:17] Modify product: Probable FKBP-type peptidyl-prolyl cis-trans isomerase FkpA => putative FKBP-type peptidyl-prolyl cis-trans isomerase FkpA
  [18:57:17] Modify product: Putative zinc metalloprotease aq_1964 => Putative zinc metalloprotease
  [18:57:17] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
  [18:57:17] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein
  [18:57:17] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC
  [18:57:17] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN
  [18:57:17] Modify product: Probable butyrate:acetyl-CoA coenzyme A-transferase => putative butyrate:acetyl-CoA coenzyme A-transferase
  [18:57:17] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO
  [18:57:17] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
  [18:57:17] Modify product: Probable transcriptional regulatory protein HP_0162 => putative transcriptional regulatory protein
  [18:57:17] Modify product: Probable bifunctional oligoribonuclease and PAP phosphatase NrnA => putative bifunctional oligoribonuclease and PAP phosphatase NrnA
  [18:57:17] Modify product: UPF0758 protein YsxA => hypothetical protein
  [18:57:17] Modify product: 23S rRNA 5-hydroxycytidine C2501 synthase => 23S rRNA 5-hydroxycytidine synthase
  [18:57:17] Modify product: UPF0194 membrane protein YbhG => hypothetical protein
  [18:57:17] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
  [18:57:17] Modify product: Probable sulfoacetate transporter SauU => putative sulfoacetate transporter SauU
  [18:57:17] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase
  [18:57:17] Modify product: Probable branched-chain-amino-acid aminotransferase => putative branched-chain-amino-acid aminotransferase
  [18:57:17] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI
  [18:57:17] Modify product: UPF0353 protein Rv1481 => hypothetical protein
  [18:57:17] Modify product: UPF0353 protein Rv1481 => hypothetical protein
  [18:57:18] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS
  [18:57:18] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH
  [18:57:18] Modify product: UPF0371 protein DIP2346 => hypothetical protein
  [18:57:18] Modify product: UPF0053 protein HI_0107 => hypothetical protein
  [18:57:18] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase
  [18:57:18] Modify product: Tricorn protease homolog 1 => Tricorn protease 
  [18:57:18] Modify product: Probable L-galactonate transporter => putative L-galactonate transporter
  [18:57:18] Modify product: UPF0701 protein HI_0467 => hypothetical protein
  [18:57:18] Modify product: Uncharacterized protein YhaP => putative protein YhaP
  [18:57:18] Modify product: Uncharacterized protein YqeN => putative protein YqeN
  [18:57:18] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
  [18:57:18] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
  [18:57:18] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
  [18:57:18] Modify product: Uncharacterized epimerase/dehydratase SA0511 => putative epimerase/dehydratase
  [18:57:18] Modify product: Putative 2-hydroxyacid dehydrogenase HI_1556 => Putative 2-hydroxyacid dehydrogenase
  [18:57:18] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 2 => putative glycine dehydrogenase (decarboxylating) subunit 2
  [18:57:18] Modify product: Probable chromate transport protein => putative chromate transport protein
  [18:57:18] Modify product: Probable manganese efflux pump MntP => putative manganese efflux pump MntP
  [18:57:18] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
  [18:57:18] Modify product: RutC family protein HI_0719 => RutC family protein
  [18:57:18] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 1 => putative glycine dehydrogenase (decarboxylating) subunit 1
  [18:57:18] Modify product: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog => Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit 
  [18:57:18] Cleaned 45 /product names
  [18:57:18] Deleting unwanted file: MGYG000000030_prokka/MGYG000000030.sprot.tmp.115.faa
  [18:57:18] Deleting unwanted file: MGYG000000030_prokka/MGYG000000030.sprot.tmp.115.blast
  [18:57:18] There are still 1050 unannotated CDS left (started with 1689)
  [18:57:18] Will use hmmer3 to search against /usr/local/db/hmm/HAMAP.hmm with 8 CPUs
  [18:57:18] Running: cat MGYG000000030_prokka\/MGYG000000030\.HAMAP\.hmm\.tmp\.115\.faa | parallel --gnu --plain -j 8 --block 23723 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /usr/local/db/hmm/HAMAP.hmm /dev/stdin > MGYG000000030_prokka\/MGYG000000030\.HAMAP\.hmm\.tmp\.115\.hmmer3 2> /dev/null
  [18:57:23] Could not run command: cat MGYG000000030_prokka\/MGYG000000030\.HAMAP\.hmm\.tmp\.115\.faa | parallel --gnu --plain -j 8 --block 23723 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /usr/local/db/hmm/HAMAP.hmm /dev/stdin > MGYG000000030_prokka\/MGYG000000030\.HAMAP\.hmm\.tmp\.115\.hmmer3 2> /dev/null

The file MGYG000000000.HAMAP.hmm.tmp.115.faa seems to be fine:

>1
MERSGFSTRLGFILVSAGCAIGLGNVWRFPYITGQYGGASFVLIYLLFLAILGLPIMVAEFAVGRASIRSAAMSFDVLEPKGTKWHWHKYTAIGGNMILMMFYTTVAGWMLYYLYKTATGAFDGLDAAGIGAVFGDLLQDPVTMGGYMAAIVLLCGGVCYLGVEAGVERITKWMMTCLLLLMVILGINSVLLPGAGEGLKYYLYPDFGRLMEHGLKEVIFAAMGQAFFTLSIGMGSLAVFGSYIGKSKRLTGEAVWIIILDTFVAIMAGLIIFPACFSYGVSPSSGPNLLFVTLPNVFNAMPLGRLWGTLFFLFMTFAAMSTVIAVFENLVVCFFDLLRIDRHKIICAGMPIVILLSLPCVLGFNEWSWIQPLGKGSGILDLEDFLVSNNILPLGSLVYMAFCTSRYGWGWDNFIKEADTGRGMEFPKWIRFYVTYILPLIVLVIFVNGYYALFFSR
>2
MAILLVITAILALIHLYHLSDKMKRLDYVYLMVLLIVMGLNTDNADYAAYERIYQKVSYATTWEEIMRAHTDKGYVFLNWLATVIGMDYKCFHLGLFTLLLGGIFIIAKRIGTPICALFLAYTMYPMFMDAIQIRNFIISAVLLFSIYCYAHANVRWYAIGVISLTIAVTIHPFILIFIPFIVFYKMYDTERFRPITYIPICLGLLSIAIKILIDTYWNEVTAMLTVLADWASRGHSYIGHQVLTSRQFKIYLVVVIFAWLLYKAKKYLSTSECVNDIQKKFVELSFVAFLYLICWMPLFALDINLATRMPRDLFLVAYMSLGIYLSKCTSQRIKIGLLFGIMFLAFFFGLVDLYISTDRFNVDVILSHNLLL
>3
MHIILVGPEYYNYSEGIISAFISLGCEVDFFPSVEFYENCSWYQRRLYKLGYKSLEKIWNNDWETRFREFIANRIRKDTIFLFCTGNMISVRLLKDLDAYVKVLYMWDSVKRYSDDFQSRLKLYDYLFAFEFGDIEFVRKKYGVSMQYMPLGYDSDFYYPDDNVVKDIDISFVGSCTKMRMNLLEKVAR
.....

[amardeepranu]

A little more insight: this works fine when running with singularity - no error, however consistently seeing failures on docker

[mberacochea]

Hi @amardeepranu

How are you running the pipeline? Locally, in an HPC cluster using a scheduler?

Cheers

[willownine]

prokka is showing 'prokka --setupdb' while running a sequence ,what is the solution for this