hecatomb combine not working

[gregorykrice]

Running "hecatomb combine --comb SRR4295172/hecatomb.out --comb SRR4295173/hecatomb.out --comb SRR4295174/hecatomb.out --comb SRR4295175/hecatomb.out --output combined_output"

[2024:03:07 10:57:15] Config file combined_output/hecatomb.config.yaml already exists. Using existing config file. [2024:03:07 10:57:15] Updating config file with new values [2024:03:07 10:57:15] Writing config file to combined_output/hecatomb.config.yaml [2024:03:07 10:57:15] ------------------ [2024:03:07 10:57:15] | Runtime config | [2024:03:07 10:57:15] ------------------

hecatomb: addHost: minViralAlnLen: 1000 args: comb:

• SRR4295172/hecatomb.out
• SRR4295173/hecatomb.out
• SRR4295174/hecatomb.out
• SRR4295175/hecatomb.out combineRuns:
• SRR4295172/hecatomb.out
• SRR4295173/hecatomb.out
• SRR4295174/hecatomb.out
• SRR4295175/hecatomb.out conda_prefix: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda configfile: combined_output/hecatomb.config.yaml example_profile: false log: combined_output/hecatomb.log output: combined_output profile: null simulate: false snake_args: [] system_config: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/config/config.yaml system_workflow_profile: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/profile/default/config.yaml threads: 12 use_conda: true workflow_profile: combined_output/hecatomb.profile assembly: canu: correctedErrorRate=0.16 maxInputCoverage=10000 minInputCoverage=0 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 useGrid=False stopOnLowCoverage=False genomeSize=10M -nanopore flye: -g 1g megahit: --presets meta-large metaflye: --meta -g 1g --nano-raw mmseqs: fast: -s 4 filtAA: --min-length 30 -e 1e-5 filtNT: --min-length 90 -e 1e-20 linclustParams: --kmer-per-seq-scale 0.3 -c 0.8 --cov-mode 1 --min-seq-id 0.97 --alignment-mode 3 sensitive: --start-sens 2 --sens-steps 3 -s 7 taxIdIgnore: 0 1 2 10239 131567 12429 2759 resources: big: cpu: 12 mem: 128000 time: '24:00:00' lrg: cpu: 8 mem: 32000 time: 04:00:00 med: cpu: 8 mem: 16000 time: 04:00:00 ram: cpu: 2 mem: 16000 time: 04:00:00 sml: cpu: 1 mem: 2000 time: 01:00:00 trimnami: qc: compression: 1 cutadapt: -m 40 fastp: --qualified_quality_phred 15 --length_required 90 --cut_tail --cut_tail_window_size 25 --cut_tail_mean_quality 15 --dedup --dup_calc_accuracy 4 --trim_poly_x --detect_adapter_for_pe filtlong: --min_length 1000 --keep_percent 95 hostRemoveFlagstat: -f 4 -F 3584 minimapIndex: -I 8G prinseq: -min_len 60 -min_qual_mean 25 -ns_max_n 1 -derep 1 -out_format 0 -trim_tail_left 5 -trim_tail_right 5 -ns_max_n 5 -trim_qual_type min -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 10

[2024:03:07 10:57:15] Config file combined_output/hecatomb.profile/config.yaml already exists. Using existing config file. [2024:03:07 10:57:15] --------------------- [2024:03:07 10:57:15] | Snakemake command | [2024:03:07 10:57:15] ---------------------

snakemake -s /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk --configfile combined_output/hecatomb.config.yaml --cores 12 --use-conda --conda-prefix /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda --workflow-profile combined_output/hecatomb.profile Using profile combined_output/hecatomb.profile and workflow specific profile combined_output/hecatomb.profile for setting default command line arguments. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/config.yaml is extended by additional config specified via the command line. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/dbFiles.yaml is extended by additional config specified via the command line. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/immutable.yaml is extended by additional config specified via the command line. No/missing assembly files for SRR4295172/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295173/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295174/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295175/hecatomb.out, skipping assembly files. TypeError in file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/rules/preflight/contig_mapping.smk, line 8: unsupported operand type(s) for +: 'NoneType' and 'str' File "/opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk", line 52, in File "/opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/rules/preflight/contig_mapping.smk", line 8, in [2024:03:07 10:57:15] ERROR: Snakemake failed

The comb directories have results/merged_assembly.fasta files, but it looks like combineOutputs.smk is expecting assembly.fasta files.

[beardymcjohnface]

This might be a simple fix. Can you please try and update the combined_output/hecatomb.config.yaml file? I think you just need to add a config setting:

hecatomb:
    args:
+        assembly: merged

If that works I'll push a fix for the next release. I also need to add build tests for this workflow at some point.

[gregorykrice]

[2024:03:13 11:51:59] Config file combined_output/hecatomb.config.yaml already exists. Using existing config file. [2024:03:13 11:51:59] Updating config file with new values [2024:03:13 11:51:59] Writing config file to combined_output/hecatomb.config.yaml [2024:03:13 11:51:59] ------------------ [2024:03:13 11:51:59] | Runtime config | [2024:03:13 11:51:59] ------------------

hecatomb: addHost: minViralAlnLen: 1000 args: assembly: merged comb:

• SRR4295172/hecatomb.out
• SRR4295173/hecatomb.out
• SRR4295174/hecatomb.out
• SRR4295175/hecatomb.out combineRuns:
• SRR4295172/hecatomb.out
• SRR4295173/hecatomb.out
• SRR4295174/hecatomb.out
• SRR4295175/hecatomb.out conda_prefix: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda configfile: combined_output/hecatomb.config.yaml example_profile: false log: combined_output/hecatomb.log output: combined_output profile: null simulate: false snake_args: [] system_config: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/config/config.yaml system_workflow_profile: /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/profile/default/config.yaml threads: 12 use_conda: true workflow_profile: combined_output/hecatomb.profile assembly: canu: correctedErrorRate=0.16 maxInputCoverage=10000 minInputCoverage=0 corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 useGrid=False stopOnLowCoverage=False genomeSize=10M -nanopore flye: -g 1g megahit: --presets meta-large metaflye: --meta -g 1g --nano-raw mmseqs: fast: -s 4 filtAA: --min-length 30 -e 1e-5 filtNT: --min-length 90 -e 1e-20 linclustParams: --kmer-per-seq-scale 0.3 -c 0.8 --cov-mode 1 --min-seq-id 0.97 --alignment-mode 3 sensitive: --start-sens 2 --sens-steps 3 -s 7 taxIdIgnore: 0 1 2 10239 131567 12429 2759 resources: big: cpu: 12 mem: 128000 time: '24:00:00' lrg: cpu: 8 mem: 32000 time: 04:00:00 med: cpu: 8 mem: 16000 time: 04:00:00 ram: cpu: 2 mem: 16000 time: 04:00:00 sml: cpu: 1 mem: 2000 time: 01:00:00 trimnami: qc: compression: 1 cutadapt: -m 40 fastp: --qualified_quality_phred 15 --length_required 90 --cut_tail --cut_tail_window_size 25 --cut_tail_mean_quality 15 --dedup --dup_calc_accuracy 4 --trim_poly_x --detect_adapter_for_pe filtlong: --min_length 1000 --keep_percent 95 hostRemoveFlagstat: -f 4 -F 3584 minimapIndex: -I 8G prinseq: -min_len 60 -min_qual_mean 25 -ns_max_n 1 -derep 1 -out_format 0 -trim_tail_left 5 -trim_tail_right 5 -ns_max_n 5 -trim_qual_type min -trim_qual_left 30 -trim_qual_right 30 -trim_qual_window 10

[2024:03:13 11:51:59] Config file combined_output/hecatomb.profile/config.yaml already exists. Using existing config file. [2024:03:13 11:51:59] --------------------- [2024:03:13 11:51:59] | Snakemake command | [2024:03:13 11:51:59] ---------------------

snakemake -s /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk --configfile combined_output/hecatomb.config.yaml --cores 12 --use-conda --conda-prefix /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/conda --workflow-profile combined_output/hecatomb.profile Using profile combined_output/hecatomb.profile and workflow specific profile combined_output/hecatomb.profile for setting default command line arguments. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/config.yaml is extended by additional config specified via the command line. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/dbFiles.yaml is extended by additional config specified via the command line. Config file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/../config/immutable.yaml is extended by additional config specified via the command line. No/missing assembly files for SRR4295172/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295173/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295174/hecatomb.out, skipping assembly files. No/missing assembly files for SRR4295175/hecatomb.out, skipping assembly files. KeyError in file /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk, line 162: 'resources' File "/opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk", line 162, in [2024:03:13 11:51:59] ERROR: Snakemake failed

awk 'NR>=161 && NR<=163 {print}' /opt/mambaforge/envs/hecatomb/lib/python3.12/site-packages/hecatomb/snakemake/workflow/combineOutputs.smk threads: config["resources"]["med"]["cpu"] resources:

[beardymcjohnface]

I think there are a couple of things I need to fix. I'll see if I can get it done this week.