nf-core / nf-core/denovotranscript

Busco TypeError: only 0-dimensional arrays can be converted to Python scalars

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Description

Description of the bug

Busco command failed:

TypeError: only 0-dimensional arrays can be converted to Python scalars

It think it is related to: [BUSCO 6.0.0 crashes in AutoLineage.evaluate() with NumPy 2.4](https://gitlab.com/ezlab/busco/-/work_items/840

I tried downgrading numpy to version 2.3.5 to fix the issue. I use another conda environment instead of modules/nf-core/busco/busco/environment.yml :

name: busco_busco
channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::busco=5.7.1
  - conda-forge::numpy=2.3.5

It fixed the particular TypeError. However, this did not help since I got this another error: IndexError: list index out of range

My last attempt at fixing the issue was to use Busco 6.0.0 as well as pinning numpy to 2.3.5 but I ran into another issue (see: SegFault in pplacer on Debian when using conda / singularity. Finally, the pipeline ran successfully after pinning sepp to 4.5.6 as well:

name: busco_busco
channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::busco=6.0.0
  - conda-forge::numpy=2.3.5
  - bioconda::sepp=4.5.6
Command used and terminal output
nextflow run nf-core/denovotranscript \
        -r 1.2.1 \
        -params-file /home/soye/dev/projects/redalgae_rna/config/params_denovotranscript.yaml \
        --input /home/soye/dev/projects/redalgae_rna/data/per_sample_sheets/WW.csv \
        --outdir /home/soye/dev/projects/redalgae_rna/data/results/denovotranscript/WW \
        -c /home/soye/dev/projects/redalgae_rna/config/nextflow.config.denovotranscript \
        -profile mamba \
        -work-dir ./work/ \
        -resume



ERROR ~ Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)'

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (1)


Command executed:

  # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
  # Check for container variable initialisation script and source it.
  if [ -f "/usr/local/env-activate.sh" ]; then
      set +u  # Otherwise, errors out because of various unbound variables
      . "/usr/local/env-activate.sh"
      set -u
  fi
  
  # If the augustus config directory is not writable, then copy to writeable area
  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
      # Create writable tmp directory for augustus
      AUG_CONF_DIR=$( mktemp -d -p $PWD )
      cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR
      export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR
      echo "New AUGUSTUS_CONFIG_PATH=${AUGUSTUS_CONFIG_PATH}"
  fi
  
  # Ensure the input is uncompressed
  INPUT_SEQS=input_seqs
  mkdir "$INPUT_SEQS"
  cd "$INPUT_SEQS"
  for FASTA in ../tmp_input/*; do
      if [ "${FASTA##*.}" == 'gz' ]; then
          gzip -cdf "$FASTA" > $( basename "$FASTA" .gz )
      else
          ln -s "$FASTA" .
      fi
  done
  cd ..
  
  busco \
      --cpu 6 \
      --in "$INPUT_SEQS" \
      --out all_assembled-auto-busco \
      --mode transcriptome \
      --auto-lineage \
       \
       \
  
  
  # clean up
  rm -rf "$INPUT_SEQS"
  
  # Move files to avoid staging/publishing issues
  mv all_assembled-auto-busco/batch_summary.txt all_assembled-auto-busco.batch_summary.txt
  mv all_assembled-auto-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO":
      busco: $( busco --version 2>&1 | sed 's/^BUSCO //' )
  END_VERSIONS

Command exit status:
  1

Command output:
  2026-05-06 09:30:11 INFO:	[hmmsearch]	6 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	11 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	16 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	21 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	27 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	32 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	42 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	47 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	52 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	Results:	C:33.1%[S:22.6%,D:10.5%],F:6.5%,M:60.4%,n:124	   
  
  2026-05-06 09:30:11 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz'
  2026-05-06 09:30:18 INFO:	Decompressing file 'busco_downloads/lineages/eukaryota_odb10.tar.gz'
  2026-05-06 09:30:19 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2024-01-08)
  2026-05-06 09:30:20 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:30:20
  2026-05-06 09:34:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:34:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:34:35 INFO:	Running 255 job(s) on hmmsearch, starting at 05/06/2026 09:34:35
  2026-05-06 09:34:36 INFO:	[hmmsearch]	26 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	51 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	77 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	102 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	128 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	153 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	179 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	204 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	230 of 255 task(s) completed
  2026-05-06 09:34:42 INFO:	[hmmsearch]	255 of 255 task(s) completed
  2026-05-06 09:34:43 INFO:	658 exons in total
  2026-05-06 09:34:43 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:34:43 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
  2026-05-06 09:34:44 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:34:44
  2026-05-06 09:42:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:42:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:42:35 INFO:	Running 50 job(s) on hmmsearch, starting at 05/06/2026 09:42:35
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   

Command error:
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:42:37 CRITICAL:	Unhandled exception occurred:
  Traceback (most recent call last):
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 120, in run
      self.get_lineage()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 65, in get_lineage
      ) = self.auto_select_lineage()  # full path
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 86, in auto_select_lineage
      asl.run_auto_selector()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 110, in run_auto_selector
      self.get_best_match_lineage(root_runners)
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 238, in get_best_match_lineage
      max_ind = self.evaluate(runners, use_percent)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 222, in evaluate
      return int(max_ind)
             ^^^^^^^^^^^^
  TypeError: only 0-dimensional arrays can be converted to Python scalars
  
  
  2026-05-06 09:42:37 ERROR:	only 0-dimensional arrays can be converted to Python scalars
  2026-05-06 09:42:37 ERROR:	BUSCO analysis failed!
  2026-05-06 09:42:37 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Work dir:
  /home/soye/dev/projects/redalgae_rna/data/run/denovotranscript/102_79/work/b6/0d84c3a5ec26415920561f0563329e

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

executor >  local (1)
[6a/e8aff5] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (102_79)  [100%] 1 of 1, cached: 1 ✔
[54/e29c84] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP (102_79)       [100%] 1 of 1, cached: 1 ✔
[f8/ff0933] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (102_79) [100%] 1 of 1, cached: 1 ✔
[cd/bed041] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ (pooled_reads)                     [100%] 1 of 1, cached: 1 ✔
[a2/540a87] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)                        [100%] 1 of 1, cached: 1 ✔
[eb/45d62f] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT (all_assembled)                      [100%] 1 of 1, cached: 1 ✔
[fe/bed89e] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS (all_assembled)             [100%] 1 of 1, cached: 1 ✔
[34/fa9be9] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled)                      [100%] 1 of 1, cached: 1 ✔
[b6/0d84c3] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)                  [  0%] 0 of 1 ✘
[ab/dd588d] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled)                     [100%] 1 of 1, cached: 1 ✔
[9b/e8d1bd] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX (all_assembled.okay.mrna)       [100%] 1 of 1, cached: 1 ✔
[67/4234de] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT (102_79)                        [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC                                      -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)'

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (1)


Command executed:

  # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
  # Check for container variable initialisation script and source it.
  if [ -f "/usr/local/env-activate.sh" ]; then
      set +u  # Otherwise, errors out because of various unbound variables
      . "/usr/local/env-activate.sh"
      set -u
  fi
  
  # If the augustus config directory is not writable, then copy to writeable area
  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
      # Create writable tmp directory for augustus
      AUG_CONF_DIR=$( mktemp -d -p $PWD )
      cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR
      export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR
      echo "New AUGUSTUS_CONFIG_PATH=${AUGUSTUS_CONFIG_PATH}"
  fi
  
  # Ensure the input is uncompressed
  INPUT_SEQS=input_seqs
  mkdir "$INPUT_SEQS"
  cd "$INPUT_SEQS"
  for FASTA in ../tmp_input/*; do
      if [ "${FASTA##*.}" == 'gz' ]; then
          gzip -cdf "$FASTA" > $( basename "$FASTA" .gz )
      else
          ln -s "$FASTA" .
      fi
  done
  cd ..
  
  busco \
      --cpu 6 \
      --in "$INPUT_SEQS" \
      --out all_assembled-auto-busco \
      --mode transcriptome \
      --auto-lineage \
       \
       \
  
  
  # clean up
  rm -rf "$INPUT_SEQS"
  
  # Move files to avoid staging/publishing issues
  mv all_assembled-auto-busco/batch_summary.txt all_assembled-auto-busco.batch_summary.txt
  mv all_assembled-auto-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO":
      busco: $( busco --version 2>&1 | sed 's/^BUSCO //' )
  END_VERSIONS

Command exit status:
  1

Command output:
  2026-05-06 09:30:11 INFO:	[hmmsearch]	6 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	11 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	16 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	21 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	27 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	32 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	42 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	47 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	52 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	Results:	C:33.1%[S:22.6%,D:10.5%],F:6.5%,M:60.4%,n:124	   
  
  2026-05-06 09:30:11 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz'
  2026-05-06 09:30:18 INFO:	Decompressing file 'busco_downloads/lineages/eukaryota_odb10.tar.gz'
  2026-05-06 09:30:19 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2024-01-08)
  2026-05-06 09:30:20 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:30:20
  2026-05-06 09:34:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:34:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:34:35 INFO:	Running 255 job(s) on hmmsearch, starting at 05/06/2026 09:34:35
  2026-05-06 09:34:36 INFO:	[hmmsearch]	26 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	51 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	77 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	102 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	128 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	153 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	179 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	204 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	230 of 255 task(s) completed
  2026-05-06 09:34:42 INFO:	[hmmsearch]	255 of 255 task(s) completed
  2026-05-06 09:34:43 INFO:	658 exons in total
  2026-05-06 09:34:43 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:34:43 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
  2026-05-06 09:34:44 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:34:44
  2026-05-06 09:42:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:42:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:42:35 INFO:	Running 50 job(s) on hmmsearch, starting at 05/06/2026 09:42:35
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   

Command error:
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:42:37 CRITICAL:	Unhandled exception occurred:
  Traceback (most recent call last):
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 120, in run
      self.get_lineage()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 65, in get_lineage
      ) = self.auto_select_lineage()  # full path
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 86, in auto_select_lineage
      asl.run_auto_selector()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 110, in run_auto_selector
      self.get_best_match_lineage(root_runners)
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 238, in get_best_match_lineage
      max_ind = self.evaluate(runners, use_percent)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 222, in evaluate
      return int(max_ind)
             ^^^^^^^^^^^^
  TypeError: only 0-dimensional arrays can be converted to Python scalars
  
  
  2026-05-06 09:42:37 ERROR:	only 0-dimensional arrays can be converted to Python scalars
  2026-05-06 09:42:37 ERROR:	BUSCO analysis failed!
  2026-05-06 09:42:37 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Work dir:
  /home/soye/dev/projects/redalgae_rna/data/run/denovotranscript/102_79/work/b6/0d84c3a5ec26415920561f0563329e

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

executor >  local (1)
[6a/e8aff5] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (102_79)  [100%] 1 of 1, cached: 1 ✔
[54/e29c84] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP (102_79)       [100%] 1 of 1, cached: 1 ✔
[f8/ff0933] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (102_79) [100%] 1 of 1, cached: 1 ✔
[cd/bed041] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ (pooled_reads)                     [100%] 1 of 1, cached: 1 ✔
[a2/540a87] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)                        [100%] 1 of 1, cached: 1 ✔
[eb/45d62f] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT (all_assembled)                      [100%] 1 of 1, cached: 1 ✔
[fe/bed89e] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS (all_assembled)             [100%] 1 of 1, cached: 1 ✔
[34/fa9be9] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled)                      [100%] 1 of 1, cached: 1 ✔
[b6/0d84c3] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)                  [  0%] 0 of 1 ✘
[ab/dd588d] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled)                     [100%] 1 of 1, cached: 1 ✔
[9b/e8d1bd] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX (all_assembled.okay.mrna)       [100%] 1 of 1, cached: 1 ✔
[67/4234de] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT (102_79)                        [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC                                      [  0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/denovotranscript] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)'

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (1)


Command executed:

  # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
  # Check for container variable initialisation script and source it.
  if [ -f "/usr/local/env-activate.sh" ]; then
      set +u  # Otherwise, errors out because of various unbound variables
      . "/usr/local/env-activate.sh"
      set -u
  fi
  
  # If the augustus config directory is not writable, then copy to writeable area
  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
      # Create writable tmp directory for augustus
      AUG_CONF_DIR=$( mktemp -d -p $PWD )
      cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR
      export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR
      echo "New AUGUSTUS_CONFIG_PATH=${AUGUSTUS_CONFIG_PATH}"
  fi
  
  # Ensure the input is uncompressed
  INPUT_SEQS=input_seqs
  mkdir "$INPUT_SEQS"
  cd "$INPUT_SEQS"
  for FASTA in ../tmp_input/*; do
      if [ "${FASTA##*.}" == 'gz' ]; then
          gzip -cdf "$FASTA" > $( basename "$FASTA" .gz )
      else
          ln -s "$FASTA" .
      fi
  done
  cd ..
  
  busco \
      --cpu 6 \
      --in "$INPUT_SEQS" \
      --out all_assembled-auto-busco \
      --mode transcriptome \
      --auto-lineage \
       \
       \
  
  
  # clean up
  rm -rf "$INPUT_SEQS"
  
  # Move files to avoid staging/publishing issues
  mv all_assembled-auto-busco/batch_summary.txt all_assembled-auto-busco.batch_summary.txt
  mv all_assembled-auto-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO":
      busco: $( busco --version 2>&1 | sed 's/^BUSCO //' )
  END_VERSIONS

Command exit status:
  1

Command output:
  2026-05-06 09:30:11 INFO:	[hmmsearch]	6 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	11 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	16 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	21 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	27 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	32 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	42 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	47 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	[hmmsearch]	52 of 52 task(s) completed
  2026-05-06 09:30:11 INFO:	Results:	C:33.1%[S:22.6%,D:10.5%],F:6.5%,M:60.4%,n:124	   
  
  2026-05-06 09:30:11 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz'
  2026-05-06 09:30:18 INFO:	Decompressing file 'busco_downloads/lineages/eukaryota_odb10.tar.gz'
  2026-05-06 09:30:19 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2024-01-08)
  2026-05-06 09:30:20 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:30:20
  2026-05-06 09:34:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:34:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:34:35 INFO:	Running 255 job(s) on hmmsearch, starting at 05/06/2026 09:34:35
  2026-05-06 09:34:36 INFO:	[hmmsearch]	26 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	51 of 255 task(s) completed
  2026-05-06 09:34:37 INFO:	[hmmsearch]	77 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	102 of 255 task(s) completed
  2026-05-06 09:34:38 INFO:	[hmmsearch]	128 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	153 of 255 task(s) completed
  2026-05-06 09:34:39 INFO:	[hmmsearch]	179 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	204 of 255 task(s) completed
  2026-05-06 09:34:40 INFO:	[hmmsearch]	230 of 255 task(s) completed
  2026-05-06 09:34:42 INFO:	[hmmsearch]	255 of 255 task(s) completed
  2026-05-06 09:34:43 INFO:	658 exons in total
  2026-05-06 09:34:43 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:34:43 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
  2026-05-06 09:34:44 INFO:	Running 1 job(s) on metaeuk, starting at 05/06/2026 09:34:44
  2026-05-06 09:42:34 INFO:	[metaeuk]	1 of 1 task(s) completed
  2026-05-06 09:42:35 INFO:	***** Run HMMER on gene sequences *****
  2026-05-06 09:42:35 INFO:	Running 50 job(s) on hmmsearch, starting at 05/06/2026 09:42:35
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   

Command error:
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  /home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/bin/busco:25: SyntaxWarning: invalid escape sequence '\w'
    "cannot import name '(?P<module_name>[\w]+)", err.msg
  2026-05-06 09:42:35 INFO:	[hmmsearch]	5 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	10 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	15 of 50 task(s) completed
  2026-05-06 09:42:35 INFO:	[hmmsearch]	20 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	25 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	30 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	35 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	40 of 50 task(s) completed
  2026-05-06 09:42:36 INFO:	[hmmsearch]	45 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	[hmmsearch]	50 of 50 task(s) completed
  2026-05-06 09:42:37 INFO:	6 candidate overlapping regions found
  2026-05-06 09:42:37 INFO:	414 exons in total
  2026-05-06 09:42:37 INFO:	Results:	C:80.4%[S:44.3%,D:36.1%],F:11.4%,M:8.2%,n:255	   
  
  2026-05-06 09:42:37 CRITICAL:	Unhandled exception occurred:
  Traceback (most recent call last):
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 120, in run
      self.get_lineage()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 65, in get_lineage
      ) = self.auto_select_lineage()  # full path
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoRunner.py", line 86, in auto_select_lineage
      asl.run_auto_selector()
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
      self.retval = func(*args, **kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 110, in run_auto_selector
      self.get_best_match_lineage(root_runners)
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 238, in get_best_match_lineage
      max_ind = self.evaluate(runners, use_percent)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/soye/dev/projects/redalgae_rna/.conda/env-8bb29e342eb405f4cd0aabfd338c5f4b/lib/python3.12/site-packages/busco/AutoLineage.py", line 222, in evaluate
      return int(max_ind)
             ^^^^^^^^^^^^
  TypeError: only 0-dimensional arrays can be converted to Python scalars
  
  
  2026-05-06 09:42:37 ERROR:	only 0-dimensional arrays can be converted to Python scalars
  2026-05-06 09:42:37 ERROR:	BUSCO analysis failed!
  2026-05-06 09:42:37 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Work dir:
  /home/soye/dev/projects/redalgae_rna/data/run/denovotranscript/102_79/work/b6/0d84c3a5ec26415920561f0563329e

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
Relevant files

No response

System information
  • nextflow 25.10.4
  • Desktop (AMD Ryzen Threadripper 3970X 32-Core)
  • local
  • mamba
  • linux (Debian GNU/Linux 12.13 (bookworm) x86_64)
  • denovotranscript 1.2.1

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the BUSCO process and its modules/nf-core/busco/busco/environment.yml dependency definition. Inspect busco/AutoLineage.py around evaluate() and busco/BuscoRunner.py around auto_select_lineage(), then reproduce the failure using the reported Nextflow command or work directory. Done means the BUSCO auto-lineage step completes without the reported TypeError in the supported environment.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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