#C02FC6VFQG1 Hello, I got the below execution report after I ran this command line: nextflow run nf-core/metatdenovo -profile conda --input samplesheet.csv --assembler megahit --save_bam --save_samtools --orf_caller prokka --eukulele_dbpath path/to/db /home/nspmpego/microbiota_photoperiodism/metatranscriptomics/eggnog/ --outdir results/ --email "myemail". Is the command ok? I am unsure about the --eukelele_path command. What does the error in the execution report mean, and how can I fix it? Any help would be greatly appreciated. The exit status of the task that caused the workflow execution to fail was: null. The full error message was: Error executing process > 'NFCORE_METATDENOVOMETATDENOVOSUB_EUKULELE:EUKULELE_SEARCH (megahit.prokka)' Caused by: Process exceeded running time limit (16h) Command executed: rc=0 mkdir contigs gunzip -c prokka.faa.gz > ./contigs/proteins.faa EUKulele \ -m mets \ \ --protein_extension .faa \ --reference_dir db \ -o megahit.prokka_[] \ --CPUs 12 \ -s \ contigs || rc=$? gzip megahit.prokka_[]/mets_full/diamond/*.out find megahit.prokka_[]/ -name "*.csv" | xargs gzip gzip megahit.prokka_[]/taxonomy_estimation/*.out cat <<-END_VERSIONS > versions.yml "NFCORE_METATDENOVOMETATDENOVOSUB_EUKULELE:EUKULELE_SEARCH": eukulele: $(echo $(EUKulele --version 2>&1) | sed -n 's/.* \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p') END_VERSIONS if [ $rc -le 1 ]; then exit 0 else exit $rc; fi Command exit status: - Command output: (empty) Work dir: /home/nspmpego/microbiota_photoperiodism/metatranscriptomics/ld_sd_meta/work/f2/6ff4027d94eb82d726802074e2bd6d Tip: view the complete command output by changing to the process work dir and entering the command

cat .command.out

The workflow was completed at 2026-05-13T052144.895650384+01:00 (duration: 1d 15h 46m 41s) (edited) execution_report_2026-05-11_13-35-01.html

The

Process exceeded running time limit (16h)

is probably key. Try extending the time limit for Eukulele with a config file similar to the below:

process {
    withName: EUKULELE_SEARCH {
        time = 48.h
    }
}

You can pass config files in different ways: https://nf-co.re/docs/running/configuration/configuration-options#custom-configuration-files I always just create a

nextflow.config

file in the directory from which I run Nextflow.

@Daniel Lundin Ok thanks I'll try to do that.

@Daniel Lundin can the config file be just a text file? Cheers,

#C02FC6VFQG1 ok now nothing is working.... I have updated nf-core version and metadenovo version and then I triend using the -c command to extend eukelele time but now I get the message below....... help: N E X T F L O W ~ version 26.04.1 WARN: Cannot read project manifest -- Cause: Config parsing failed WARN: This Nextflow version supports a new Multi-revision strategy for managing the SCM repositories, but 'nf-core/metatdenovo' is single-revision legacy strategy - Please consider to update the repository with the 'nextflow pull -migrate' command. Error nextflow.config37235:

manifest

is not defined │ 372 | \033[0;35m nf-core/metatdenovo ${manifest.version}\033[0m ╰ | ^^^^^^^^ Error nextflow.config37526:

manifest

is not defined │ 375 | afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${ma ╰ | ^^^^^^^^ Error nextflow.config37569:

manifest

is not defined │ 375 | ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " ╰ | ^^^^^^^^ Error nextflow.config375186:

manifest

is not defined │ 375 | doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} ╰ | ^^^^^^^^ Error nextflow.config38422:

validation

is not defined │ 384 | beforeText = validation.help.beforeText ╰ | ^^^^^^^^^^ Error nextflow.config38521:

validation

is not defined │ 385 | afterText = validation.help.afterText ╰ | ^^^^^^^^^^ ERROR ~ Config parsing failed

I'm currently running metadenovo, but I'm not sure if its getting stuck. This keeps getting repeated in the

.nextflow.log

file:

May-18 17:40:09.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 2; name: NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_DOWNLOAD (KEGG data); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/2e/9e301a22b0b42e2e197c59b044bea0]
~> TaskHandler[id: 48; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_Gpacif_1); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/89/fb88013d478dcb40a5b1f5d28adff1]
~> TaskHandler[id: 7; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (control_Atam); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/f8/3456f0ee4635cef898e027ac115aff]
~> TaskHandler[id: 46; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GexcentExtra); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/50/cde2a2c834cf8871a5819fe115171e]
~> TaskHandler[id: 17; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (control_BBenv); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/7f/249a7d70d818e3ea8962fb9c25e534]
~> TaskHandler[id: 22; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (control_Omarina); status: RUNNING; exit: -; error: -; workDir: /home/ec2-user/work/06/3ddc798d6eead41a45a0fee0a93a67]
May-18 17:41:11.949 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 42 -- tasks to be submitted are shown below
~> TaskHandler[id: 28; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GaustExtra); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/03/8223a4c1dcd2d0874a30964855053a]
~> TaskHandler[id: 44; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_Gcarib); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/f6/2138fcf4c410167af69c0c0cb92c43]
~> TaskHandler[id: 23; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (control_Phoff); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/e5/d1af4dee040adcefa863a72d5152c4]
~> TaskHandler[id: 5; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (control_Amon); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/02/6b3ef990c1605bb71b92a6f7cdb120]
~> TaskHandler[id: 38; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GspRII_MixedPRexp); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/9c/7921d220799ceaa0ede2219b4eefe4]
~> TaskHandler[id: 35; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GexcentLog); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/14/b7d78f0503d69bcdaa8119f2310394]
~> TaskHandler[id: 45; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_Gsilvae); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/94/147910b19835e0a72a5734d53312ae]
~> TaskHandler[id: 32; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GexcentExp); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/6c/32c2dc7d3f237fad2592f88a656457]
~> TaskHandler[id: 37; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GspRII_1655log); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/b1/437c667dc44d2e9dd53a1e7c3ef58e]
~> TaskHandler[id: 42; name: NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:FASTQC (experimental_GspRII_MixedPRlog); status: NEW; exit: -; error: -; workDir: /home/ec2-user/work/83/a3a499b2f5b1ded088091a7fe19061]
.. remaining tasks omitted.

Hello, I am trying to run the 1.3.0 metaTdenovo pipeline on 3 eukaryotic metatranscriptomic samples, using megahit assembler and transdecoder ORF caller. Everything went quite smoothly until the functionnal annotation step. The pipeline stops while trying to do the Kofamscan annotation, with the following error message.

ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN (megahit.transdecoder)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN (megahit.transdecoder)` terminated with an error exit status (1)


Command executed:

  exec_annotation \
      --profile profiles \
      --ko-list ko_list \
      --format detail-tsv \
      --cpu 24 \
      megahit_assembly.contigs.fa.transdecoder.pep \
      -o kofamscan_output.tsv

  # Create a cleaned up version for summary_tables
  echo "orfguerikometaT_thrshld0scoreestevaluesiko_definition" | gzip -c > kofamscan.tsv.gz
  grep -v '#' kofamscan_output.tsv | cut -f 2-7|sed 's/ "/      /' | sed 's/"$//' | gzip -c >> kofamscan.tsv.gz

  # Gzip the original file
  gzip kofamscan_output.tsv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN":
      kofamscan: $(echo $(exec_annotation --version 2>&1) | sed 's/^.*exec_annotation//' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  /usr/local/bin/lib/kofam_scan/parallel.rb:28:in `write': Broken pipe (Errno::EPIPE)
        from /usr/local/bin/lib/kofam_scan/parallel.rb:28:in `puts'
        from /usr/local/bin/lib/kofam_scan/parallel.rb:28:in `block in exec'
        from /usr/local/lib/ruby/2.7.0/open3.rb:219:in `popen_run'
        from /usr/local/lib/ruby/2.7.0/open3.rb:101:in `popen3'
        from /usr/local/bin/lib/kofam_scan/parallel.rb:27:in `exec'
        from /usr/local/bin/lib/kofam_scan/executor.rb:107:in `run_hmmsearch'
        from /usr/local/bin/lib/kofam_scan/executor.rb:35:in `execute'
        from /usr/local/bin/lib/kofam_scan/executor.rb:8:in `execute'
        from /usr/local/bin/lib/kofam_scan/cli.rb:21:in `run'
        from /usr/local/bin/exec_annotation:7:in `<main>'

Work dir:
  /scratch/guerin/metaT_vigo/210526_test/work/0b/c22502a2b90c1bd4429fcc7936e5b5

Container:
  /scratch/guerin/metaT_vigo/210526_test/work/singularity/depot.galaxyproject.org-singularity-kofamscan-1.3.0--hdfd78af_2.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

I have seen that people had similar problems in the past. I tried to change the

versions.yml

file, that looked like this:

"NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_DOWNLOAD":
    wget: 1.21.4

to make it look like this, as it was recommended on one of the previous threads:

"NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN":
    kofamscan:  1.3.0

But I got the same error message. I tried to manually download KofamScan DB like described on the usage page of the pipeline and adding a

versions.yml

file, but got the same error again. I wonder if it could be linked to this reported bug? https://github.com/nf-core/metatdenovo/issues/365 I am getting stop on this issue, I re launched my test while skipping kofam annotation and it is running, but I would like to have it implemented at the end. Do you have any idea on what I could try to overcome this issue? Did some of you have met the same issue ? Thank you in advance for your help, Best regards, Nina Guerin

#metadenovo, hello. I am having continuing problems with this pipeline. I am not sure that I understand what the issue is, but I wanted to ask a question about the pipeline script. I had to download the eukulele phylodb database and I used the following command to create the files needed > create_protein_table.py --infile_peptide reference.pep.fa \ --infile_taxonomy taxonomy-table.txt --outfile_json prot-map.json \ --output tax-table.txt --delim "/" --col_source_id Source_ID \ --taxonomy_col_id taxonomy --column SOURCE_ID The files are in a folder called "phylodb". In the nexflow metadenovo pipeline should I use --eukulele_dbpath ./phylodb \ or should the folder phylodb be moved in the eukulele folder? and should I use --eukulele_db phylodb \ or anything else? Any help will be greatly appreciated.

Hello, I tried to launch the pipeline on my full dataset of samples (46 eukaryotic metaT samples) and it stopped at the step of MEGAHIT_INTERLEAVED. From what I understand, the error come is "Cannot allocate memory" but I am not sure if the problem comes from the pipeline and how I launched it or if it comes from hardware requirements. I am launching the job on my institute calculation cluster, and I checked I still have a lot of storage remaining on my scratch space, and I was planning larger on my cluster allocation. I admit that I am not extremely knowledgeable on how the cluster works precisely. Please find attached the error message outputted by the pipeline. I will also attached in comment my launcher.sh and config.custom files, along with the memory left on my scratch space. Thank you for the time you'll give to my question!

ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:MEGAHIT_INTERLEAVED (megahit_assembly)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:MEGAHIT_INTERLEAVED (megahit_assembly)` terminated with an error exit status (1)


Command executed:

  megahit \
      --12 SAMEA112488779.processed.fastq.gz,SAMEA112488781.processed.fastq.gz,SAMEA112488783.processed.fastq.gz,SAMEA112488785.processed.fastq.gz,SAMEA112488787.processed.fastq.gz,SAMEA112488789.processed.fastq.gz,SAMEA112533980.processed.fastq.gz,SAMEA112533978.processed.fastq.gz,SAMEA112533982.processed.fastq.gz,SAMEA112533984.processed.fastq.gz,SAMEA112534048.processed.fastq.gz,SAMEA112534054.processed.fastq.gz,SAMEA112534052.processed.fastq.gz,SAMEA112534084.processed.fastq.gz,SAMEA112534082.processed.fastq.gz,SAMEA112534088.processed.fastq.gz,SAMEA112534086.processed.fastq.gz,SAMEA112534090.processed.fastq.gz,SAMEA112534120.processed.fastq.gz,SAMEA112534158.processed.fastq.gz,SAMEA112534156.processed.fastq.gz,SAMEA112534160.processed.fastq.gz,SAMEA112534162.processed.fastq.gz,SAMEA112534164.processed.fastq.gz,SAMEA112534216.processed.fastq.gz,SAMEA112534214.processed.fastq.gz,SAMEA112534218.processed.fastq.gz,SAMEA112534220.processed.fastq.gz,SAMEA112534224.processed.fastq.gz,SAMEA112534222.processed.fastq.gz,SAMEA112534050_1.processed.fastq.gz,SAMEA112534046_1.processed.fastq.gz,SAMEA112534056_1.processed.fastq.gz,SAMEA112534083_1.processed.fastq.gz,SAMEA112534087_1.processed.fastq.gz,SAMEA112534085_1.processed.fastq.gz \
       \
      -t 24 \
      -m 154618822656 \
       \
      --out-prefix megahit_assembly

  pigz \
      --no-name \
      -p 24 \
       \
      megahit_out/*.fa \
      megahit_out/intermediate_contigs/*.fa

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:MEGAHIT_INTERLEAVED":
      megahit_interleaved: $(echo $(megahit -v 2>&1) | sed 's/MEGAHIT v//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  2026-06-24 17:43:30 - MEGAHIT v1.2.9
  2026-06-24 17:43:30 - Using megahit_core with POPCNT and BMI2 support
  2026-06-24 17:43:30 - Convert reads to binary library
  2026-06-24 17:56:27 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (SAMEA112488779.processed.fastq.gz): interleaved, 330969846 reads, 151 max length'
  2026-06-24 18:12:47 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 1 (SAMEA112488781.processed.fastq.gz): interleaved, 418061500 reads, 151 max length'
  2026-06-24 18:23:55 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 2 (SAMEA112488783.processed.fastq.gz): interleaved, 281697330 reads, 151 max length'
  2026-06-24 18:42:26 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 3 (SAMEA112488785.processed.fastq.gz): interleaved, 443171510 reads, 151 max length'
  2026-06-24 18:56:50 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 4 (SAMEA112488787.processed.fastq.gz): interleaved, 366504792 reads, 151 max length'
  2026-06-24 19:10:44 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 5 (SAMEA112488789.processed.fastq.gz): interleaved, 353437134 reads, 151 max length'
  2026-06-24 19:20:14 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 6 (SAMEA112533980.processed.fastq.gz): interleaved, 242509428 reads, 151 max length'
  2026-06-24 19:29:52 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 7 (SAMEA112533978.processed.fastq.gz): interleaved, 247484254 reads, 151 max length'
  2026-06-24 19:37:18 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 8 (SAMEA112533982.processed.fastq.gz): interleaved, 194677678 reads, 151 max length'
  2026-06-24 19:45:24 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 9 (SAMEA112533984.processed.fastq.gz): interleaved, 210388086 reads, 151 max length'
  2026-06-24 19:53:38 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 10 (SAMEA112534048.processed.fastq.gz): interleaved, 216787134 reads, 151 max length'
  2026-06-24 20:02:11 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 11 (SAMEA112534054.processed.fastq.gz): interleaved, 219249356 reads, 151 max length'
  2026-06-24 20:10:30 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 12 (SAMEA112534052.processed.fastq.gz): interleaved, 210772632 reads, 151 max length'
  2026-06-24 20:21:57 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 13 (SAMEA112534084.processed.fastq.gz): interleaved, 293333894 reads, 151 max length'
  2026-06-24 20:31:21 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 14 (SAMEA112534082.processed.fastq.gz): interleaved, 241679850 reads, 151 max length'
  2026-06-24 20:45:54 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 15 (SAMEA112534088.processed.fastq.gz): interleaved, 346717592 reads, 151 max length'
  2026-06-24 20:56:44 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 16 (SAMEA112534086.processed.fastq.gz): interleaved, 274343836 reads, 151 max length'
  2026-06-24 21:09:33 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 17 (SAMEA112534090.processed.fastq.gz): interleaved, 311296626 reads, 151 max length'
  2026-06-24 21:22:05 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 18 (SAMEA112534120.processed.fastq.gz): interleaved, 306036610 reads, 151 max length'
  2026-06-24 21:33:48 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 19 (SAMEA112534158rk/8f/897094b394572f98a3d80b7b58600a/SAMEA112534158.processed.fastq.gz): interleaved, 285230734 reads, 151 max length'
  2026-06-24 21:45:27 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 20 (SAMEA112534156.processed.fastq.gz): interleaved, 279968728 reads, 151 max length'
  2026-06-24 22:11:02 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 21 (SAMEA112534160.processed.fastq.gz): interleaved, 660008944 reads, 151 max length'
  2026-06-24 22:19:48 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 22 (SAMEA112534162.processed.fastq.gz): interleaved, 226245252 reads, 151 max length'
  2026-06-24 22:34:35 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 23 (SAMEA112534164.processed.fastq.gz): interleaved, 346805916 reads, 151 max length'
  2026-06-24 22:44:40 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 24 (SAMEA112534216.processed.fastq.gz): interleaved, 260460298 reads, 151 max length'
  2026-06-24 22:55:34 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 25 (SAMEA112534214.processed.fastq.gz): interleaved, 285244160 reads, 151 max length'
  2026-06-24 23:07:38 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 26 (SAMEA112534218.processed.fastq.gz): interleaved, 286147632 reads, 151 max length'
  2026-06-24 23:17:04 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 27 (SAMEA112534220.processed.fastq.gz): interleaved, 221833914 reads, 151 max length'
  2026-06-24 23:27:11 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 28 (SAMEA112534224.processed.fastq.gz): interleaved, 252437182 reads, 151 max length'
  2026-06-24 23:38:35 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 29 (SAMEA112534222.processed.fastq.gz): interleaved, 276737726 reads, 151 max length'
  2026-06-24 23:55:50 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 30 (SAMEA112534050_1.processed.fastq.gz): interleaved, 450255760 reads, 151 max length'
  2026-06-25 00:11:27 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 31 (SAMEA112534046_1.processed.fastq.gz): interleaved, 406221836 reads, 151 max length'
  2026-06-25 00:24:06 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 32 (SAMEA112534056_1.processed.fastq.gz): interleaved, 299051760 reads, 151 max length'
  2026-06-25 00:42:21 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 33 (SAMEA112534083_1.processed.fastq.gz): interleaved, 458899136 reads, 151 max length'
  2026-06-25 01:00:28 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 34 (SAMEA112534087_1.processed.fastq.gz): interleaved, 441589610 reads, 151 max length'
  2026-06-25 01:18:29 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 35 (SAMEA112534085_1.processed.fastq.gz): interleaved, 478353932 reads, 151 max length'
  2026-06-25 01:18:29 - b'INFO  utils/utils.h                 :  152 - Real: 27299.1916\tuser: 9465.8391\tsys: 1201.8240\tmaxrss: 250132'
  2026-06-25 01:18:29 - k-max reset to: 141
  2026-06-25 01:18:29 - Start assembly. Number of CPU threads 24
  2026-06-25 01:18:29 - k list: 21,29,39,59,79,99,119,141
  2026-06-25 01:18:29 - Memory used: 154618822656
  2026-06-25 01:18:29 - Extract solid (k+1)-mers for k = 21
  .command.run: fork: Cannot allocate memory
  2026-06-25 01:46:04 - Error occurs, please refer to megahit_out/megahit_assembly.log for detail
  2026-06-25 01:46:04 - Command: /usr/local/bin/megahit_core count -k 21 -m 2 --host_mem 154618822656 --mem_flag 1 --output_prefix megahit_out/tmp/k21/21 --num_cpu_threads 24 --read_lib_file megahit_out/tmp/reads.lib; Exit code -9
  .command.run: line 180: kill: (37) - No such process

Work dir:
  /scratch/guerin/metaT_vigo/190626_euk/work/8f/897094b394572f98a3d80b7b58600a

Container:
  /scratch/guerin/metaT_vigo/190626_euk/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99-8ec213d21e5d03f9db54898a2baeaf8ec729b447-0.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

<!channel>: Finally a new release! 1.4.0 deals with the problems some of you've had with downloads: 1) that the eggNOG database doesn't download through the pipeline (now it does, I hope) and 2) that local databases still triggered download (they don't any more). Plus other bug fixes, upgrades of tools and the nf-core template. Thanks to all involved including some key reviewers: @James Fellows Yates, @Charles Plessy, @Daniel Straub plus a new contributor: Teresa Rubio. Changelog here: https://github.com/nf-core/metatdenovo/blob/master/CHANGELOG.md

❌ metatdenovo/test_full failed 😿 Run Name boring_brown Duration 7h 20m 38s Status ❌ Failed Error Message

2:14PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
2:14PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-03f255787fe851d48 instance-type=c6id.12xlarge
2:14PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
2:19PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.8TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 1059.51MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3590.53MB, drops:1766, skip:0, sync:13, req:41

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name boring_brown -params-file '<https://api.cloud.seqera.io/ephemeral/ge1k8tmMZfZU6HYturhCaw.json>' -with-tower -r dev -profile test_full

Jun 26, 2026 at 2:19 PM

❌ metatdenovo/test_full failed 😿 Run Name fabulous_magritte Duration 10h 5m 8s Status ❌ Failed Error Message

6:16PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
6:16PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-03b90c577da32220f instance-type=r6id.24xlarge
6:16PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
grep: write error: Broken pipe
6:21PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:5.7TB, min:5.6TB, max:5.7TB, end:5.6TB
    clone_namespace: false
    download: 1059.51MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.12-8ea351d
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3723.90MB, drops:0, skip:0, sync:14, req:43

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name fabulous_magritte -params-file '<https://api.cloud.seqera.io/ephemeral/98OIEhUpmQVMVgcxLwrkvw.json>' -with-tower -r dev -profile test_full

Jun 26, 2026 at 6:22 PM

❌ metatdenovo/test_full failed 😿 Run Name astonishing_lavoisier Duration 5h 20m 6s Status ❌ Failed Error Message

2026-06-26 14:45:58 - MEGAHIT v1.2.9
2026-06-26 14:45:59 - Using megahit_core with POPCNT and BMI2 support
2026-06-26 14:45:59 - Convert reads to binary library
2026-06-26 14:47:10 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/fusion/s3/nf-core-awsmegatests/work/metatdenovo/work-4d0307aa7d34575aa7891a7b4996ffe19e774cd9/9f/467bd1fc700aad17bed2e84015d437/ERR978615.processed.fastq.gz): interleaved, 40525544 reads, 101 max length'
2026-06-26 14:48:31 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 1 (/fusion/s3/nf-core-awsmegatests/work/metatdenovo/work-4d0307aa7d34575aa7891a7b4996ffe19e774cd9/9f/467bd1fc700aad17bed2e84015d437/ERR978616.processed.fastq.gz): interleaved, 45305414 reads, 101 max length'
2026-06-26 14:50:59 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 2 (/fusion/s3/nf-core-awsmegatests/work/metatdenovo/work-4d0307aa7d34575aa7891a7b4996ffe19e774cd9/9f/467bd1fc700aad17bed2e84015d437/ERR978614.processed.fastq.gz): interleaved, 83969516 reads, 101 max length'
2026-06-26 14:53:40 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 3 (/fusion/s3/nf-core-awsmegatests/work/metatdenovo/work-4d0307aa7d34575aa7891a7b4996ffe19e774cd9/9f/467bd1fc700aad17bed2e84015d437/ERR978612.processed.fastq.gz): interleaved, 91205786 reads, 101 max length'
2026-06-26 14:53:40 - b'INFO  utils/utils.h                 :  152 - Real: 461.8109\tuser: 129.5027\tsys: 36.2367\tmaxrss: 281384'
2026-06-26 14:53:40 - k-max reset to: 119 
2026-06-26 14:53:40 - Start assembly. Number of CPU threads 1 
2026-06-26 14:53:40 - k list: 21,29,39,59,79,99,119 
2026-06-26 14:53:40 - Memory used: 214748364800
2026-06-26 14:53:40 - Extract solid (k+1)-mers for k = 21 
2026-06-26 16:56:58 - Build graph for k = 21 
2026-06-26 17:03:01 - Assemble contigs from SdBG for k = 21
2026-06-26 17:52:17 - Local assembly for k = 21
2026-06-26 17:59:32 - Extract iterative edges from k = 21 to 29 
2026-06-26 18:20:10 - Build graph for k = 29 
2026-06-26 18:23:17 - Assemble contigs from SdBG for ...

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name astonishing_lavoisier -params-file '<https://api.cloud.seqera.io/ephemeral/nNvNpUDyK_AA8JQM4_dvmg.json>' -with-tower -r 4d0307aa7d34575aa7891a7b4996ffe19e774cd9 -profile test_full

Jun 26, 2026 at 6:47 PM

I've gotten farther than in the previous version, but I'm still getting errors.

Dear #C02FC6VFQG1 people, what do I need to do to put mag in #C02FC6VFQG1, cf https://github.com/nf-core/fetchngs/issues/376

I was able to gain access to a different cluster and it's going further, but now it's erroring out in the SPAdes assembly. Is there something I can change that can fix this?

Hi, I am running an nf-core/metatdenovo workflow on the HPC system, and the BBNorm step fails after approximately 41 hours while trying to write its normalized FASTQ output. The job successfully completed the k-mer counting/hash-table construction: • BBNorm memory allocation: 819 GB • Hash table: ~598 GB • Estimated unique k-mers: ~211 billion • Hash-table occupancy: 86.08% • Table creation time: ~147,067 s (~41 h) The process then fails with: java.io.IOException: Cannot run program “bgzip”: /scratch/SlurmTMP/userID.23778641/TEMPFILE_BBNORM_P1_R1_11cf4e18dc999d13e904e68b23d0cc__62875.239315649414.fq.gz (No such file or directory) Caused by: java.io.FileNotFoundException: /scratch/SlurmTMP/userID.23778641/TEMPFILE_BBNORM_P1_R1_11cf4e18dc999d13e904e68b23d0cc__62875.239315649414.fq.gz (No such file or directory) Exception in thread “main” java.lang.AssertionError: Could not execute bgzip -c -f -l 4 -@ 6 The BBNorm command is: bbnorm.sh in=<~100 FASTQ files> out=all_samples.fastq.gz target=50 min=5 threads=6 -Xmx819g The process is running inside the nf-core/metatdenovo Singularity container. I have verified that bgzip is present inside the container: /opt/conda/bin/bgzip bgzip (htslib) 1.21 and /opt/conda/bin is in the container PATH. BBNorm itself does not explicitly set a temporary directory. The error indicates that it is attempting to use: /scratch/SlurmTMP/userID.23778641/ for a temporary FASTQ file. An initial check shows no node or filesystem problems on the node used. Could this be a Singularity problem (i.e. that you have to mount/connect the external directories to some internal container overlays)?

❌ metatdenovo/test_full failed 😿 Run Name special_shannon Duration 2h 4m 54s Status ❌ Failed Error Message

12:00PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
12:00PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-08baa8f407b53e052 instance-type=r6id.12xlarge
12:00PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
12:05PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.6TB, min:2.5TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 1059.49MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3687.34MB, drops:0, skip:0, sync:13, req:41

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name special_shannon -params-file '<https://api.cloud.seqera.io/ephemeral/fdwVNujld222yN4VQEP-IQ.json>' -with-tower -r dev -profile test_full

Sep 15, 2026 at 12:05 PM

Patch release 1.4.1 fixing the problem with paths not mounted by Singularity: github.com/nf-core/metatdenovo/…/1.4.1. To run this release:

nextflow pull nf-core/metatdenovo -r 1.4.1
nextflow run nf-core/metatdenovo -r 1.4.1 -profile <...> --outdir  <...> <other params

❌ metatdenovo/test_full failed 😿 Run Name elated_saha Duration 1h 47m 31s Status ❌ Failed Error Message

2:52PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
2:52PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-082fcb68915b8758c instance-type=m6id.12xlarge
2:52PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
2:57PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.8TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 1059.49MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3690.15MB, drops:0, skip:0, sync:13, req:41

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name elated_saha -params-file '<https://api.cloud.seqera.io/ephemeral/tj5d_t2fKSY1wbupzEPXYw.json>' -with-tower -r dev -profile test_full

Sep 15, 2026 at 2:58 PM

❌ metatdenovo/test_full failed 😿 Run Name pedantic_poincare Duration 6h 45m 55s Status ❌ Failed Error Message

9:15PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
9:15PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-09c51255c41280896 instance-type=r6id.12xlarge
9:15PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
9:20PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:2.8TB, min:2.8TB, max:2.8TB, end:2.8TB
    clone_namespace: false
    download: 1059.51MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3702.22MB, drops:0, skip:0, sync:13, req:41

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name pedantic_poincare -params-file '<https://api.cloud.seqera.io/ephemeral/oP0mT2DxmI1ZXYjuvPci6A.json>' -with-tower -r 113adb3c3e5dc04ac0df9041a4cb001c838dd830 -profile test_full

Sep 15, 2026 at 9:20 PM

❌ metatdenovo/test_full failed 😿 Run Name tiny_gilbert Duration 8m 35s Status ❌ Failed Error Message

(more omitted..)
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.01G/5.13G [03:14<00:04, 24.2MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.02G/5.13G [03:14<00:04, 24.9MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.02G/5.13G [03:14<00:04, 25.4MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.02G/5.13G [03:15<00:04, 25.8MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.03G/5.13G [03:15<00:04, 26.0MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.03G/5.13G [03:15<00:03, 26.2MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.03G/5.13G [03:15<00:03, 26.3MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.04G/5.13G [03:15<00:03, 26.5MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.04G/5.13G [03:15<00:03, 26.1MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.04G/5.13G [03:15<00:03, 26.2MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.05G/5.13G [03:15<00:03, 26.4MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.05G/5.13G [03:16<00:03, 26.5MiB/s]
Downloading dbCAN-sub.hmm:  98%|█████████▊| 5.05G/5.13G [03:16<00:03, 26.5MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▊| 5.06G/5.13G [03:16<00:02, 26.6MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▊| 5.06G/5.13G [03:16<00:02, 26.5MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▊| 5.06G/5.13G [03:16<00:02, 26.6MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▊| 5.06G/5.13G [03:16<00:02, 26.6MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▊| 5.07G/5.13G [03:16<00:02, 26.6MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.07G/5.13G [03:16<00:02, 23.3MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.07G/5.13G [03:17<00:02, 24.2MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.08G/5.13G [03:17<00:02, 24.9MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.08G/5.13G [03:17<00:02, 25.4MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.08G/5.13G [03:17<00:01, 25.8MiB/s]
Downloading dbCAN-sub.hmm:  99%|█████████▉| 5.09G/5.13G [03:17<00:01, 26.0MiB/s]
Downloading dbCAN-sub.hmm:  99%|███████...

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name tiny_gilbert -params-file '<https://api.cloud.seqera.io/ephemeral/TJI6AP76ldxAPIIELfGKtg.json>' -with-tower -r dev -profile test_full

Sep 27, 2026 at 4:43 PM

❌ metatdenovo/test_full failed 😿 Run Name sharp_thompson Duration 41.1s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/metatdenovo>, projectDir: /.nextflow/assets/.repos/nf-core/metatdenovo/clones/ae9302f1dcee00630986dff9997e4119bcc4a6a6, commitId: ae9302f1dcee00630986dff9997e4119bcc4a6a6, revision: dev, startTime: 2026-10-07T08:08:40.496353718Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/metatdenovo>' -name sharp_thompson -params-file '<https://api.cloud.seqera.io/ephemeral/imU0woLCDXqXy8Qdm2CXeA.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@4ff3af97, enable:nextflow.NextflowMeta$Features@5680f009, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/metatdenovo/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name sharp_thompson -params-file '<https://api.cloud.seqera.io/ephemeral/imU0woLCDXqXy8Qdm2CXeA.json>' -with-tower -r dev -profile test_full

Oct 7, 2026 at 8:09 AM

2.0.0 released! Release notes are here: github.com/nf-core/metatdenovo/…/2.0.0 Many thanks to contributors: @Danilo Di Leo, @Phil Ewels, @mashehu, @Jonathan Manning, @Maxime Garcia, @Lea Picard (leapfroggie_), @James Fellows Yates, @piplus2, @Niklas Schandry, @Evangelos Karatzas, @Jonas S, @Joon Klaps, @Trace Lail and @Luis Heinzlmeier!

❌ metatdenovo/test_full failed 😿 Run Name exotic_joliot Duration 1h 54m 23s Status ❌ Failed Error Message

11:40AM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
11:40AM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-04dbe264c7330c644 instance-type=r6id.4xlarge
11:40AM INF [seqera-fusion] starting incremental snapshot timer interval=300000
11:45AM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:943GB, min:911GB, max:943GB, end:921GB
    clone_namespace: false
    download: 2083.49MB, drops:0, skip:0, sync:0, req:17
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 6134.15MB, drops:0, skip:0, sync:13, req:60

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name exotic_joliot -params-file '<https://api.cloud.seqera.io/ephemeral/9WoyJ327mlyASVIWA7rZ5w.json>' -with-tower -r e9f8311e9a24278fdaed0f8717eb819532aef55e -profile test_full

Oct 7, 2026 at 11:45 AM

❌ metatdenovo/test_full failed 😿 Run Name elated_mccarthy Duration 1h 52m 38s Status ❌ Failed Error Message

4:03PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
4:03PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0080a193991e1705d instance-type=r6id.4xlarge
4:03PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
4:08PM INF [seqera-fusion] sending incremental snapshot signal (SIGUSR1)
FUSION_GPU_USED=false
Fusion Info:
    available_disk: start:943GB, min:923GB, max:943GB, end:930GB
    clone_namespace: false
    download: 1059.49MB, drops:0, skip:0, sync:0, req:9
    fusion_version: 2.5.14-20e904e
    kernel_version: 6.1
    max_open_files: 1048576
    upload: 3451.41MB, drops:557, skip:0, sync:13, req:39

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name elated_mccarthy -params-file '<https://api.cloud.seqera.io/ephemeral/yaZAdKOWO99zlLQ2CHnx7Q.json>' -with-tower -r e9f8311e9a24278fdaed0f8717eb819532aef55e -profile test_full

Oct 7, 2026 at 4:08 PM

❌ metatdenovo/test_full failed 😿 Run Name stoic_heisenberg Duration 2h 16m 54s Status ❌ Failed Error Message

(more omitted..)
[21:50:23] Modify product: Probable serine/threonine-protein kinase PkwA => putative serine/threonine-protein kinase PkwA
[21:50:23] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[21:50:23] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
[21:50:23] Modify product: UPF0178 protein YaiI => hypothetical protein
[21:50:23] Modify product: UPF0301 protein SO_3346 => hypothetical protein
[21:50:23] Modify product: Probable TonB-dependent siderophore receptor PirA => putative TonB-dependent siderophore receptor PirA
[21:50:23] Modify product: UPF0145 protein YbjQ => hypothetical protein
[21:50:23] Modify product: Probable iron-sulfur-binding oxidoreductase FadF => putative iron-sulfur-binding oxidoreductase FadF
[21:50:23] Modify product: Uncharacterized protein PA3435 => putative protein
[21:50:23] Modify product: Putative zinc metalloprotease PA3649 => Putative zinc metalloprotease
[21:50:23] Modify product: Uncharacterized ABC transporter ATP-binding protein YadG => putative ABC transporter ATP-binding protein YadG
[21:50:23] Modify product: Probable acyl-CoA dehydrogenase FadE2 => putative acyl-CoA dehydrogenase FadE2
[21:50:23] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO
[21:50:23] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[21:50:23] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[21:50:23] Modify product: Protein Rv1367c => Protein
[21:50:24] Modify product: Uncharacterized metal-dependent hydrolase YjjV => putative metal-dependent hydrolase YjjV
[21:50:24] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG
[21:50:24] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
[21:50:24] Modify product: Probable manganese-dependent i...

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name stoic_heisenberg -params-file '<https://api.cloud.seqera.io/ephemeral/N0V8IiUb2b1ZTXQlAWNm3Q.json>' -with-tower -r 0e9aac97762aab6276ab6bc3a28bdef7fc20815b -profile test_full

Oct 7, 2026 at 9:52 PM

❌ metatdenovo/test_full failed 😿 Run Name stoic_saha Duration 2h 51m 10s Status ❌ Failed Error Message

(more omitted..)
8:41AM ERR [seqera-fusion] failed to delete chunk during cleanup error="operation error S3: DeleteObject, https response error StatusCode: 403, RequestID: 30M53S85DQTE1TGM, HostID: hBCYKpanoLhKSvVZzNAW7Amk69EYLh46QR8OoXUECtrleWea9T8H7hhzNklwaBfkozVqK+OdJKg=, api error AccessDenied: Access Denied" goid=1732877 id=/s3/ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/diamond/reference.pep.dmnd offset=100797513728
8:41AM ERR [seqera-fusion] failed to delete chunk during cleanup error="operation error S3: DeleteObject, https response error StatusCode: 403, RequestID: 30M1PSN06KGQ9TC0, HostID: LSGCyo7WjOph+d9pIZJDNGsjcd4N2r9BVgucWGaXxD1DHAvDXz8H4RTYD/z6zQeccwRfI+JhAlc3TA0Kuw9wyRxa37YSNEcv, api error AccessDenied: Access Denied" goid=1732877 id=/s3/ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/diamond/reference.pep.dmnd offset=100931731456
8:41AM ERR [seqera-fusion] failed to delete chunk during cleanup error="operation error S3: DeleteObject, https response error StatusCode: 403, RequestID: 30MA73BNGGN3EP83, HostID: TacmNOr1mJdl4zOrN1v914mvb8rL4awZDBcTDkFu8cg8JiiKmk8UllTnOYQco1kphq3EO4RPr6HaGamwhiHNkOXuypdpuhHz, api error AccessDenied: Access Denied" goid=1732877 id=/s3/ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/diamond/reference.pep.dmnd offset=101065949184
8:41AM ERR [seqera-fusion] failed to delete chunk during cleanup error="operation error S3: DeleteObject, https response error StatusCode: 403, RequestID: 30MDEGKTHMKQYF79, HostID: 3PZknQO/m0eVrRZrSsKLtFbyw047GBHT1OGdJPOZw/xs3VUyCsQt5Aihma6PtyZ9vmgd9x99Gp8=, api error AccessDenied: Access Denied" goid=1732877 id=/s3/ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/diamond/reference.pep.dmnd offset=101200166912
8:41AM ERR [seqera-fusion] failed to delete chunk during cleanup error="operation error S3: DeleteObject, https response error StatusCode: 403, RequestID: 30M6XXT8HW8AWH6F, HostID: 5YUsUFBAnp974orWf1vVB+fVCV6pEDNDsYidOluBp9nwhruF8tCy84dCbMoTktWKchYsSgT1MxI=, api error AccessDenied: Acce...

Command Line

nextflow run '<https://github.com/nf-core/metatdenovo>' -name stoic_saha -params-file '<https://api.cloud.seqera.io/ephemeral/lGk4UNGTGEGafcq5rCrepg.json>' -with-tower -r 75d9a7a51c514ec98a61193cdc0c7ebe01c47bbe -profile test_full

Oct 8, 2026 at 8:41 AM

Hello, I am trying to run the pipeline with the --trim_nextseq option. In Usage, the parameter is supposed to be a string, which does not make sense to me. The nf-core rnaseq 3.1 pipeline also uses the TrimGalore Module and the parameter type for the same option --trim_nextseq is an integer. nextflow run nf-core/metatdenovo -r 2.0.0 -profile singularity --input samplesheet.csv --trim_nextseq '20' Error: --trim_nextseq (20): Value is [integer] but should be [string] Thank you for your help!

Hello! with a colleague we are trying to run metatdenovo on 5 samples focusing on bacteria. I just got this error message. Should I just download gtdb and eukulele by myself or is there a simpler way? I also join our params.yml. Thank you 🙂