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I'm currently running metadenovo, but I'm not sure...
# metatdenovo
b
I'm currently running metadenovo, but I'm not sure if its getting stuck. This keeps getting repeated in the 
.nextflow.log
file:
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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.
d
This looks fine. It looks like you're using the local executor, i.e. running jobs directly on the same machine as you're running Nextflow on. This means you should see activity using e.g. 
top
for the processes Nextflow is currently running.
Are you running Nextflow interactively now? In that case, you should see processes getting done.
b
okay excellent. I canceled it as I was working on AWS and that charges by time running and if it was getting stuck I didn't want to keep running it. But that means I have the environment set up appropriately and will just let it run. Thank you so much!!
Okay, it looks like it failed. I'm having issues understand why and where. I have attached the nextflow log file and the execution report where it says what the failures are.
execution_report_2026-05-19_13-46-09.html
d
You have four processes that terminated with error status 129. I'm not sure what this is, but a little bit of googling suggests it might be that didn't have enough memory (RAM). Since you're running on AWS, this could either be because the particular processes that failed need to be allocated more memory (this is done with a config file like below) or that you didn't allocate sufficient memory for your instance. Since one of the processes that failed was 
KOFAMSCAN_DOWNLOAD
I'm a little sceptical about the memory per process explanation. This shouldn't require much memory (6 GiB allocated by default). Because I'm unfamiliar with the compute environment you're using, I don't know if the total memory explanation could be the problem. If it's not memory, it could be time.
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process {
  withName: TRIMGALORE {
    memory = 128.GB
  }
}
IIRC, you had downloaded the Kofamscan database already, so it's strange that this process is run at all. This might be due to a file called 
versions.yml
not being present in the directory. We will fix this in the next release, but in the meanwhile, create a file looking like the below and place in the download directory.
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"NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN":
    kofamscan:  1.3.0
One config thing you might want to look at, to make sure it matches your compute environment is this:
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process {
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '1.h'
    ]
}
(The values above are way below what you need.)
b
I didn't have the kofam database downloaded, so I did that and called it in. I also increased my resource limits to the max option: cpu: 64, memory: 512gb. I'll see how that runs
Now I'm getting a whole new error:
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Execution cancelled -- Finishing pending tasks before exit
-[nf-core/metatdenovo] Pipeline completed with errors-
WARN: Killing running tasks (11)
ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD (EggNOG)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD (EggNOG)` terminated with an error exit status (1)


Command executed:

  download_eggnog_data.py \
       \
      -y \
      --data_dir .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD":
      eggnog: $( echo $(emapper.py --version 2>&1)| sed 's/.* emapper-//' | sed 's/ \/ Expected.*//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  /home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/bin/download_eggnog_data.py:177: SyntaxWarning: "\." is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\."? A raw string is also an option.
    'outf=$(echo "$file" | sed "s/\.raw_alg\.faa\.gz/\.fa/"); '
  Traceback (most recent call last):
    File "/home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/bin/download_eggnog_data.py", line 6, in <module>
      from eggnogmapper.common import get_eggnogdb_file, get_ncbitaxadb_file, get_eggnog_mmseqs_dbpath, get_pfam_dbpath, get_hmmer_base_dbpath
    File "/home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/lib/python3.14/site-packages/eggnogmapper/common.py", line 6, in <module>
      from distutils.spawn import find_executable
  ModuleNotFoundError: No module named 'distutils'

Work dir:
  /home/ec2-user/work/bb/8d08faaf599c48f2f2595b51383e65

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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
ERROR ~ /home/ec2-user/s3-drive/output/pipeline_info/nf_core_metatdenovo_software_mqc_versions.yml: Operation not permitted

 -- Check '.nextflow.log' file for details
WARN: Failed to render execution report -- see the log file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
WARN: Failed to render execution timeline -- see the log file for details
This is my command:
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nextflow run nf-core/metatdenovo -profile conda -r 1.3.0 -c local_config.config --input samplesheet.csv --assembler megahit --orf_caller transdecoder --eukulele_dbpath /home/ec2-user/s3-drive/uploaded-files/eukulele --eukulele_db phylodb --eggnog_dbpath /home/ec2-user/s3-drive/uploaded-files/eggnogg --kofam_dir /home/ec2-user/s3-drive/uploaded-files/kofam --outdir ~/s3-drive/output
This is what i have in the eggnog folder
minus that .tsv file. I was messing with something after the error before I took the screenshot
d
I don't know why the pipeline failed, but you need a 
versions.yml
in the 
eggnog
directory too:
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"NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD":
    eggnog: 2.1.9
My directory looks like this:
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$ ll /data/eggnog-mapper/
total 49747152
-rw-r--r-- 1 dl data 41370988544 mar  2  2021 eggnog.db
-rw-r--r-- 1 dl data           0 okt 27  2025 eggnog.db.gz
-rw-r--r-- 1 dl data  9285439161 mar  2  2021 eggnog_proteins.dmnd
-rw-r--r-- 1 dl data           0 okt 27  2025 eggnog_proteins.dmnd.gz
-rw-r--r-- 1 dl data   278003712 nov 11  2020 eggnog.taxa.db
-rw-r--r-- 1 dl data     6628719 nov 11  2020 eggnog.taxa.db.traverse.pkl
-rw-r--r-- 1 dl data           0 okt 27  2025 eggnog.taxa.tar.gz
drwxr-sr-x 2 dl data        4096 aug 10  2022 pfam
-rw-r--r-- 1 dl data          75 okt 27  2025 versions.yml
You also seem to have some write permission problems:
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ERROR ~ /home/ec2-user/s3-drive/output/pipeline_info/nf_core_metatdenovo_software_mqc_versions.yml: Operation not permitted
Plus the one with the execution report.
See also this issue that asks to upgrade the version of the eggnog database -- and suggests how to download files in the meanwhile -- that we will deal with ASAP: https://github.com/nf-core/metatdenovo/issues/423.
b
okay, I grabbed the correct dataset now, and I'm adding a versions.yml. I'll see how that works
Okay, it's still giving me errors:
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Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD (EggNOG)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD (EggNOG)` terminated with an error exit status (1)


Command executed:

  download_eggnog_data.py \
       \
      -y \
      --data_dir .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:EGGNOG:EGGNOG_DOWNLOAD":
      eggnog: $( echo $(emapper.py --version 2>&1)| sed 's/.* emapper-//' | sed 's/ \/ Expected.*//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  /home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/bin/download_eggnog_data.py:177: SyntaxWarning: "\." is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\."? A raw string is also an option.
    'outf=$(echo "$file" | sed "s/\.raw_alg\.faa\.gz/\.fa/"); '
  Traceback (most recent call last):
    File "/home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/bin/download_eggnog_data.py", line 6, in <module>
      from eggnogmapper.common import get_eggnogdb_file, get_ncbitaxadb_file, get_eggnog_mmseqs_dbpath, get_pfam_dbpath, get_hmmer_base_dbpath
    File "/home/ec2-user/work/conda/env-e3d708a9ca94216a85c0f2948073114a/lib/python3.14/site-packages/eggnogmapper/common.py", line 6, in <module>
      from distutils.spawn import find_executable
  ModuleNotFoundError: No module named 'distutils'

Work dir:
  /home/ec2-user/work/79/3217e234d249bc758b50be6b012a55

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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
image.png,versions.yml,.nextflow.log
versions.yml.nextflow.log
Those are the files I have in my eggnog folder, and that's the versions.yml I'm using
d
You're problem is that the eggnog database download runs, right? So the above log message 
Execution cancelled
is because you canceled. Maybe you could start by specifying 
--skip_eggnog
to see if you can get the rest of the pipeline through? In the meanwhile, I'll check the files you have and compare to what the process expects.
Also, since the pipeline doesn't support later versions of the eggnog database yet, maybe running it without the eggnog tool and then run the eggnog mapper separately on the fasta file with amino acid sequences produced might be your best option at the moment. That is, assuming you prefer a later version of the tool/database.
b
okay, understood. Thank you!
I skipped eggnog but now at the end of the log file its saying its done but it doesn't give an error on the running screen
d
Isn't that good? (I'm on my phone until tomorrow so I can't look at the file.)
b
It looks like its getting stuck in some places and completing without completing
execution_report_2026-05-20_18-10-36.html
d
So, it's not doing anything? When you run -- interactively -- you should get a list of processes the pipeline aims to execute. One by one should then be ticked off. Are you not seeing that?
b
I have a couple tick off, but then it stops doing it
It looks like even though I specified the directory for kofam, its still trying to download, and I think its getting stuck there
(I reduced my samples down to 1 to test and see if I was a) overloading the system and b) reduce the noise of the lines to see where the problem might be)
d
It's a better idea to skip as many steps as you can as the assembly depends on the all samples together. So, skip kofamscan too for now but keep all samples. (If you use Prokka as gene caller you'll get a functional annotation with that.)
b
okay, I'll try that
it was definitely getting stuck there, because I am now receiving a new error as I think it moved forward:
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ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:TRIMGALORE (control_Pglacialis)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:TRIMGALORE (control_Pglacialis)` terminated with an error exit status (1)


Command executed:

  [ ! -f  control_Pglacialis_1.fastq.gz ] && ln -s MMETSP0227-Polarella-glacialis-CCMP-1383.1.fastq.gz control_Pglacialis_1.fastq.gz
  [ ! -f  control_Pglacialis_2.fastq.gz ] && ln -s MMETSP0227-Polarella-glacialis-CCMP-1383.2.fastq.gz control_Pglacialis_2.fastq.gz
  trim_galore \
      --fastqc \
      --cores 8 \
      --paired \
      --gzip \
      control_Pglacialis_1.fastq.gz \
      control_Pglacialis_2.fastq.gz

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:FASTQC_TRIMGALORE:TRIMGALORE":
      trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//')
      cutadapt: $(cutadapt --version)
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  pigz 2.8
  igzip command line interface 2.31.1

Command error:

  No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)



  AUTO-DETECTING ADAPTER TYPE
  ===========================
  Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> control_Pglacialis_1.fastq.gz <<)

  Found perfect matches for the following adapter sequences:
  Adapter type  Count   Sequence        Sequences analysed      Percentage
  Illumina      57      AGATCGGAAGAGC   1000000 0.01
  smallRNA      2       TGGAATTCTCGG    1000000 0.00
  Nextera       0       CTGTCTCTTATA    1000000 0.00
  Using Illumina adapter for trimming (count: 57). Second best hit was smallRNA (count: 2)

  Writing report to 'control_Pglacialis_1.fastq.gz_trimming_report.txt'

  SUMMARISING RUN PARAMETERS
  ==========================
  Input filename: control_Pglacialis_1.fastq.gz
  Trimming mode: paired-end
  Trim Galore version: 0.6.10
  Cutadapt version: 4.9
  Python version: could not detect
  Number of cores used for trimming: 8
  Quality Phred score cutoff: 20
  Quality encoding type selected: ASCII+33
  Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
  Maximum trimming error rate: 0.1 (default)
  Minimum required adapter overlap (stringency): 1 bp
  Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
  Running FastQC on the data once trimming has completed
  Output file(s) will be GZIP compressed

  Cutadapt seems to be fairly up-to-date (version 4.9). Setting -j 8
  Writing final adapter and quality trimmed output to control_Pglacialis_1_trimmed.fq.gz


    >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file control_Pglacialis_1.fastq.gz <<<
  This is cutadapt 4.9 with Python 3.12.13
  Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC control_Pglacialis_1.fastq.gz
  Processing single-end reads on 8 cores ...
  Error in FASTQ file at line 3: Sequence descriptions don't match ('NIKITA_0911:6:1101:1367:2245#ATCACG/1 run=120515_SN403_0911_AC0FA3ACXX' != 'NIKITA_0911:6:1101:1367:2245#ATCACG/1').
  The second sequence description must be either empty or equal to the first description.


  Cutadapt terminated with exit signal: '256'.
  Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

Work dir:
  /home/ec2-user/work/5d/dc4baa8e428b45a9734bd2bfa5fa18

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
d
It looks like your forward reads do not match up with the reverse namewise. See quite far down in the message
b
Okay. It seems that the pipeline doesn't like that sample, so I removed it to see if it will process
It errored out again, looks like at the trimming step
execution_report_2026-05-22_14-06-51.html
d
I'm on my phone so it's difficult to check your attachments. Are you sure it's not another case of forward and reverse reads not matching?
b
From what I can tell, it doesn't seem to be the case
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