Closed anugos closed 1 year ago
Hi there,
first thing that seems error prone is
Nextflow Version 21.08.0.edge
Using an edge version can get quickly out of hand, those have often bugs and are intended for developer, not for end users. Better use the latest sable release. I do not think that this is the problem though.
Your error message
[11:46:19] Running: cat MEGAHIT-group-14.13/MEGAHIT-group-14.13.IS.tmp.155872.faa | parallel --gnu --plain -j 2 --block 14971 --recstart '>' --pipe blastp -query - -db /usr/local/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > MEGAHIT-group-14.13/MEGAHIT-group-14.13.IS.tmp.155872.blast 2> /dev/null [11:46:19] Could not run command: cat MEGAHIT-group-14.13/MEGAHIT-group-14.13.IS.tmp.155872.faa | parallel --gnu --plain -j 2 --block 14971 --recstart '>' --pipe blastp -query - -db /usr/local/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > MEGAHIT-group-14.13/MEGAHIT-group-14.13.IS.tmp.155872.blast 2> /dev/null
sounds a lot like https://github.com/tseemann/prokka/issues/402 It might be possible to solve your issue with another Prokka version, by using a different container, e.g. following https://nf-co.re/mag/2.1.1/usage#updating-containers using https://bioconda.github.io/recipes/prokka/README.html or container tags https://quay.io/repository/biocontainers/prokka?tab=tags. Currently used container is https://github.com/nf-core/mag/blob/e065754c46eedc85d46cd8a71b32ad73b3b741cb/modules/nf-core/modules/prokka/main.nf#L13-L18
Hi @anugos, did you try the solution @d4straub suggested, could the problem be solved?
No it didn't work. As of now I am reassembling reads with metaspades and will retry the prokka. I will send you updates if it work this time or not. Thank you for your time. Have a nice day.
Best- Anu
On Mon, Jul 18, 2022, 08:17 Sabrina Krakau @.***> wrote:
Hi @anugos https://github.com/anugos, did you try the solution @d4straub https://github.com/d4straub suggested, could the problem be solved?
— Reply to this email directly, view it on GitHub https://github.com/nf-core/mag/issues/320#issuecomment-1187402808, or unsubscribe https://github.com/notifications/unsubscribe-auth/API7OGUQCIU3TA2FKDKCVIDVUVKQJANCNFSM5X4CQT5Q . You are receiving this because you were mentioned.Message ID: @.***>
I'm running into the same problem on a cluster when using remote execution. Running the process on a local node, even using singularity works fine for me.
Not solving you problem here, but I think we should change to https://github.com/oschwengers/bakta, because prokka seems to be not updated any more and bakta (at least from what I read) seems superior.
nf-core module exists already if someone fancies jumping on this ;)
@anugos @maxibor I had the same problem running via slurm on HPC and was able to resolve it by switching the prokka container to this one https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4
Not solving you problem here, but I think we should change to https://github.com/oschwengers/bakta, because prokka seems to be not updated any more and bakta (at least from what I read) seems superior.
i have the same issue - but using the mentioned container on slurm did not solve it for me :(
... as an addon - i tried basically every container i could find on dockerhub - always with the same file
it runs on a hpc cluster via singularity.
[it works fine to install prokka via conda and use it that way -> it only fails in the container]
@plaquette could you please supply more information e.g. commands, error messages, .nextflkow.log files etc
sure:
i tried it as part of the nf-core/bacass
pipeline.
where i used slurm as an executer on our centos 7.9 based cluster with the singularity profile and nf version 22.10.6
i tried the following containers as a replacement for the default ones:
depot.galaxyproject.org-singularity-prokka-1.14.6--pl526_0.img
depot.galaxyproject.org-singularity-prokka-1.14.6--pl5321hdfd78af_4.img
nanozoo-prokka-1.14.6--c99ff65.img
plaquette-prokka_helper-conda.img
staphb-prokka-1.13.img
staphb-prokka-1.14.0.img
staphb-prokka-1.14.6.img
staphb-prokka-latest.img
and as mentioned above - it always fails with something like this:
[12:14:00] Running: cat \/data\/ERR016613\.AMR\.tmp\.1\.faa | parallel --gnu --plain -j 4 --block 61191 --recstart '>' --pipe blastp -query - -db /root/prokka/db/kingdom/Bacteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/ERR016613\.AMR\.tmp\.1\.blast 2> /dev/null
@plaquette could you please share the .command.log
file oin the reported working
directroy of the errored profcess?
sure:
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
[11:02:49] This is prokka 1.14.6
[11:02:49] Written by Torsten Seemann <torsten.seemann@gmail.com>
[11:02:49] Homepage is https://github.com/tseemann/prokka
[11:02:49] Local time is Thu Apr 27 11:02:49 2023
[11:02:49] You are not telling me who you are!
[11:02:49] Operating system is linux
[11:02:49] You have BioPerl 1.007002
[11:02:49] System has 128 cores.
[11:02:49] Will use maximum of 1 cores.
[11:02:49] Annotating as >>> Bacteria <<<
[11:02:49] Generating locus_tag from 'ERR016616.scaffolds.fa' contents.
[11:02:49] Setting --locustag JPFOJJCG from MD5 39f833c0760e34d88161046764734911
[11:02:49] Creating new output folder: ERR016616
[11:02:49] Running: mkdir -p ERR016616
[11:02:49] Using filename prefix: ERR016616.XXX
[11:02:49] Setting HMMER_NCPU=1
[11:02:49] Writing log to: ERR016616/ERR016616.log
[11:02:49] Command: /usr/local/bin/prokka --cpus 1 --prefix ERR016616 ERR016616.scaffolds.fa
[11:02:49] Appending to PATH: /usr/local/bin
[11:02:49] Looking for 'aragorn' - found /usr/local/bin/aragorn
[11:02:49] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
[11:02:49] Looking for 'barrnap' - found /usr/local/bin/barrnap
[11:02:49] Determined barrnap version is 000009 from 'barrnap 0.9'
[11:02:49] Looking for 'blastp' - found /usr/local/bin/blastp
[11:02:50] Determined blastp version is 002009 from 'blastp: 2.9.0+'
[11:02:50] Looking for 'cmpress' - found /usr/local/bin/cmpress
[11:02:50] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
[11:02:50] Looking for 'cmscan' - found /usr/local/bin/cmscan
[11:02:50] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
[11:02:50] Looking for 'egrep' - found /bin/egrep
[11:02:50] Looking for 'find' - found /usr/bin/find
[11:02:50] Looking for 'grep' - found /bin/grep
[11:02:50] Looking for 'hmmpress' - found /usr/local/bin/hmmpress
[11:02:50] Determined hmmpress version is 003003 from '# HMMER 3.3 (Nov 2019); http://hmmer.org/'
[11:02:50] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
[11:02:50] Determined hmmscan version is 003003 from '# HMMER 3.3 (Nov 2019); http://hmmer.org/'
[11:02:50] Looking for 'java' - found /usr/local/bin/java
[11:02:50] Looking for 'makeblastdb' - found /usr/local/bin/makeblastdb
[11:02:50] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
[11:02:50] Looking for 'minced' - found /usr/local/bin/minced
[11:02:50] Determined minced version is 004002 from 'minced 0.4.2'
[11:02:50] Looking for 'parallel' - found /usr/local/bin/parallel
[11:02:50] Determined parallel version is 20200122 from 'GNU parallel 20200122'
[11:02:50] Looking for 'prodigal' - found /usr/local/bin/prodigal
[11:02:50] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
[11:02:50] Looking for 'prokka-genbank_to_fasta_db' - found /usr/local/bin/prokka-genbank_to_fasta_db
[11:02:50] Looking for 'sed' - found /bin/sed
[11:02:50] Looking for 'tbl2asn' - found /usr/local/bin/tbl2asn
[11:02:50] Determined tbl2asn version is 025007 from 'tbl2asn 25.7 arguments:'
[11:02:50] Using genetic code table 11.
[11:02:50] Loading and checking input file: ERR016616.scaffolds.fa
[11:02:50] Wrote 111 contigs totalling 1730507 bp.
[11:02:50] Predicting tRNAs and tmRNAs
[11:02:50] Running: aragorn -l -gc11 -w ERR016616\/ERR016616\.fna
[11:02:51] 1 tRNA-Met c[1033,1109] 35 (cat)
[11:02:51] 2 tRNA-Ala [137857,137932] 34 (tgc)
[11:02:51] 3 tRNA-Ile [137940,138016] 35 (gat)
[11:02:51] 1 tRNA-Gln [48018,48092] 33 (ttg)
[11:02:51] 2 tRNA-Met [48124,48199] 34 (cat)
[11:02:51] 3 tRNA-Phe c[48414,48489] 34 (gaa)
[11:02:51] 1 tRNA-Ser c[34949,35036] 35 (tga)
[11:02:51] 2 tRNA-Cys c[35068,35141] 33 (gca)
[11:02:51] 3 tRNA-Leu c[35163,35251] 35 (taa)
[11:02:51] 4 tRNA-Gly c[35262,35336] 33 (gcc)
[11:02:51] 1 tmRNA [34441,34799] 89,133 ANNVKFAPAYAKAA*
[11:02:51] 2 tRNA-Ser c[45070,45160] 35 (gct)
[11:02:51] 1 tRNA-Leu c[20914,20998] 35 (tag)
[11:02:51] 2 tRNA-Arg c[21004,21080] 35 (tct)
[11:02:51] 3 tRNA-Arg c[21095,21171] 35 (tcg)
[11:02:51] 4 tRNA-His c[21176,21252] 35 (gtg)
[11:02:51] 5 tRNA-Pro c[21277,21354] 36 (tgg)
[11:02:51] 1 tRNA-Trp c[11911,11986] 34 (cca)
[11:02:51] 2 tRNA-Thr c[13469,13543] 33 (ggt)
[11:02:51] 3 tRNA-Gly c[13638,13714] 35 (tcc)
[11:02:51] 4 tRNA-Tyr c[13721,13806] 35 (gta)
[11:02:51] 5 tRNA-Thr c[13868,13943] 34 (tgt)
[11:02:51] 1 tRNA-Asn c[25363,25437] 33 (gtt)
[11:02:51] 1 tRNA-Glu c[193,267] 34 (ttc)
[11:02:51] 1 tRNA-Leu c[9319,9404] 35 (gag)
[11:02:51] 1 tRNA-Arg [3151,3227] 35 (cct)
[11:02:51] 1 tRNA-SeC c[16493,16586] 35 (tca)
[11:02:51] 1 tRNA-Arg [13511,13587] 35 (gcg)
[11:02:51] 1 tRNA-Val c[317,392] 34 (gac)
[11:02:51] 2 tRNA-Ala c[394,469] 34 (ggc)
[11:02:51] 3 tRNA-Ser c[1679,1766] 35 (gga)
[11:02:51] 4 tRNA-Met [1871,1947] 35 (cat)
[11:02:51] Found 32 tRNAs
[11:02:51] Predicting Ribosomal RNAs
[11:02:51] Running Barrnap with 1 threads
[11:02:52] 1 1 136246 16S ribosomal RNA
[11:02:52] 2 71 621 23S ribosomal RNA
[11:02:52] Found 2 rRNAs
[11:02:52] Skipping ncRNA search, enable with --rfam if desired.
[11:02:52] Total of 33 tRNA + rRNA features
[11:02:52] Searching for CRISPR repeats
[11:02:53] CRISPR1 1 18 with 3 spacers
[11:02:53] Found 1 CRISPRs
[11:02:53] Predicting coding sequences
[11:02:53] Contigs total 1730507 bp, so using single mode
[11:02:53] Running: prodigal -i ERR016616\/ERR016616\.fna -c -m -g 11 -p single -f sco -q
[11:02:55] Excluding CDS which overlaps existing RNA (rRNA) at 71:3024..3392 on - strand
[11:02:55] Found 1723 CDS
[11:02:55] Connecting features back to sequences
[11:02:55] Not using genus-specific database. Try --usegenus to enable it.
[11:02:55] Annotating CDS, please be patient.
[11:02:55] Will use 1 CPUs for similarity searching.
[11:02:55] There are still 1723 unannotated CDS left (started with 1723)
[11:02:55] Will use blast to search against /usr/local/db/kingdom/Bacteria/IS with 1 CPUs
[11:02:55] Running: cat ERR016616\/ERR016616\.IS\.tmp\.49065\.faa | parallel --gnu --plain -j 1 --block 267740 --recstart '>' --pipe blastp -query - -db /usr/local/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > ERR016616\/ERR016616\.IS\.tmp\.49065\.blast 2> /dev/null
[11:02:55] Could not run command: cat ERR016616\/ERR016616\.IS\.tmp\.49065\.faa | parallel --gnu --plain -j 1 --block 267740 --recstart '>' --pipe blastp -query - -db /usr/local/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > ERR016616\/ERR016616\.IS\.tmp\.49065\.blast 2> /dev/null
sorry for the delayed response!
Hm the log is unfortunately not very helpful there, I'm not sure what else I can suggest @plaquette sorry :(.
nonetheless, thank you very much @jfy133 ! ... i assume its a strange centOS issue.
prokka works from conda env. but not in the container
i build (for testing purposes) a centOS specific prokka container (-> https://github.com/plaquette/prokka_container) but even this died with the same error.
(in case its relevant i tested many of the prokka containers on docker hub as well - but all with the same error as above)
Yes sounds like it :(, sorry @plaquette !
I guess we can shut this now as someone else reported the issue with the updated container (1.14.6) which we already have in the pipeline now.
We can reopen if it crops up again.
Hi, I am using NFCORE MAG for the first time and unable to understand the error I ran through with prokka. I have attached the error log below. I appreciate your help. Thanks Anu
The full error message was:
The command used to launch the workflow was as follows:
Pipeline Configuration:
https://github.com/nf-core/mag