Hello! I am running this: NXF_VER=24.10.5 nextflow run nf-core/funcscan -r 3.0.0 \ -profile apptainer \ --input input.csv --amp_skip_ampcombi_clustering \ --run_amp_screening \ --outdir output \ -resume and I am getting a strange error -[nf-core/funcscan] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_FUNCSCANFUNCSCANAMP:AMPCOMBI2_CLUSTER (ampcombi2)' Caused by: Process

NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER (ampcombi2)

terminated with an error exit status (1) Command executed: ampcombi cluster \ --ampcombi_summary Ampcombi_summary.tsv \ --cluster_cov_mode 0 --cluster_mode 1 --cluster_coverage 0.8 --cluster_seq_id 0.4 --cluster_sensitivity 4.0 --cluster_min_member 0 --log TRUE \ --threads 6 cat <<-END_VERSIONS > versions.yml "NFCORE_FUNCSCANFUNCSCANAMP:AMPCOMBI2_CLUSTER": ampcombi: $(ampcombi --version | sed 's/ampcombi //') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: ^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/computation/expressions.py", line 241, in evaluate return _evaluate(op, op_str, a, b) # type: ignore[misc] ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/computation/expressions.py", line 70, in _evaluate_standard return op(a, b) File "/usr/local/bin/clustering_hits.py", line 19, in parsing_input_for_cluster merged_df['seq_headers'] = merged_df['sample_id'] + '!' + merged_df['contig_id'] + '!' + merged_df['CDS_id'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/common.py", line 72, in new_method return method(self, other) ^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/arraylike.py", line 102, in add return self._arith_method(other, operator.add) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/series.py", line 6259, in _arith_method return base.IndexOpsMixin._arith_method(self, other, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/base.py", line 1325, in _arith_method result = ops.arithmetic_op(lvalues, rvalues, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 226, in arithmetic_op res_values = _na_arithmetic_op(left, right, op) # type: ignore[arg-type] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 172, in _na_arithmetic_op result = _masked_arith_op(left, right, op) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.11/site-packages/pandas/core/ops/array_ops.py", line 110, in _masked_arith_op result[mask] = op(xrav[mask], yrav[mask]) ^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: can only concatenate str (not "int") to str Work dir: /gpfs1/home/r/b/rbarrant/projects/simran/work/a7/e59a4f0e145b81eb2c706d01c94295 Container: /gpfs2/scratch/pi/jdragon/NXF_APPTAINER_CACHEDIR/quay.io-biocontainers-ampcombi-2.0.1--pyhdfd78af_0.img I have tried other versions of ampcombi and have had the same issue, unless the version is much older so I get other type of error. Any ideas?

markdownhelp

Using some code formatting helps with readability and finding the issue. Here are some tips about how to format code snippets nicely in Slack: http://tiny.cc/mdcodeblocks http://tiny.cc/slacksnippets

But otherwise, no I've not seen this error... @Jasmin Frangenberg any ideas?

I also tried it with the development version on a different computer and got the same error

Could you look at the contents of the input files?

Good call! Got it, the fasta files had something like:

Huh interesting, that is worth a bug report on the ampcombi repo Glad you fixed it!

Ok @James Fellows Yates, would you like me to do that?

Yes please!