CAT_pack summarise fails when a contig/bin has more than one classification #870
Description
Description of the bug
Identified in the AWS Megatest for the long-read samples.
Known limitation: https://github.com/MGXlab/CAT_pack?tab=readme-ov-file#interpreting-the-output-files
Need to work out how to check for this first so it doesn't fail...
The exit status of the task that caused the workflow execution to fail was: 1
Error executing process > 'NFCORE_MAG:MAG:CATPACK:CATPACK_SUMMARISE_BINS (CAPES_S21)'
Caused by:
Essential container in task exited
Command executed:
CAT_pack summarise \
\
-i MEGAHIT-MetaBAT2-CAPES_S21-bins_bin2classification.names.txt \
\
-o MEGAHIT-MetaBAT2-CAPES_S21-bins_summary.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:CATPACK:CATPACK_SUMMARISE_BINS":
catpack: $(CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g')
END_VERSIONS
Command exit status:
1
Command output:
# CAT_pack v6.0.
[2025-09-28 22:41:02] Summarising...
Command error:
10:41PM INF instance metadata ami-id=ami-08c9a28b806bde705 instance-id=i-02b0e90081dab791e instance-type=c6id.32xlarge
[2025-09-28 22:41:02] ERROR: some bins have multiple classifications. CAT_pack summarise currently does not allow for this. Bins with multiple classifications: MEGAHIT-MetaBAT2-CAPES_S21.15.fa.
# CAT_pack v6.0.
[2025-09-28 22:41:02] Summarising...
Fusion Info:
fusion_version: 2.4.14-93ca7f1
clone_namespace: false
kernel_version: 6.1
disk_cache_size: 7076Gb
max_open_files: 1048576
Work dir:
s3://nf-core-awsmegatests/work/mag/dev/86/c1e902b506e91bda7cc42a4b8fce9e
Container:
wave.seqera.io/wt/c0f439f3dd1a/biocontainers/cat:6.0.1--hdfd78af_1
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Command used and terminal output
Relevant files
No response
System information
No response