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May 1, 2022 16:57
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| Unlocking working directory. | |
| Building DAG of jobs... | |
| Using shell: /bin/bash | |
| Provided cluster nodes: 32 | |
| Conda environments: ignored | |
| Job stats: | |
| job count min threads max threads | |
| --------------------------------- ------- ------------- ------------- | |
| add_branch_labels 4 1 1 | |
| adjust_metadata_regions 4 1 1 | |
| align 1 8 8 | |
| all 1 1 1 | |
| ancestral 4 1 1 | |
| annotate_metadata_with_index 4 1 1 | |
| build_align 4 8 8 | |
| calculate_epiweeks 4 1 1 | |
| clades 4 1 1 | |
| colors 4 1 1 | |
| combine_input_metadata 1 1 1 | |
| combine_samples 4 1 1 | |
| combine_sequences_for_subsampling 1 1 1 | |
| diagnostic 4 1 1 | |
| distances 4 1 1 | |
| emerging_lineages 4 1 1 | |
| export 4 1 1 | |
| filter 4 1 1 | |
| finalize 4 1 1 | |
| include_hcov19_prefix 4 1 1 | |
| index 4 1 1 | |
| join_metadata_and_nextclade_qc 4 1 1 | |
| logistic_growth 4 1 1 | |
| mask 4 1 1 | |
| mutational_fitness 4 1 1 | |
| recency 4 1 1 | |
| refine 4 1 1 | |
| rename_emerging_lineages 4 1 1 | |
| sanitize_metadata 1 1 1 | |
| subsample 6 1 1 | |
| tip_frequencies 4 1 1 | |
| traits 4 1 1 | |
| translate 4 1 1 | |
| tree 4 8 8 | |
| total 123 1 8 | |
| Select jobs to execute... | |
| [Sun May 1 12:03:50 2022] | |
| Job 12: | |
| Aligning sequences to defaults/reference_seq.fasta | |
| - gaps relative to reference are considered real | |
| python3 scripts/sanitize_sequences.py --sequences data/africa_from_september.fasta --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_africa_recent.txt | nextalign --jobs=8 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b --sequences /dev/stdin --output-dir results/translations --output-basename seqs_africa_recent --output-fasta results/aligned_africa_recent.fasta --output-insertions results/insertions_africa_recent.tsv > logs/align_africa_recent.txt 2>&1; | |
| xz -2 -T 8 results/aligned_africa_recent.fasta; | |
| xz -2 -T 8 results/translations/seqs_africa_recent*.fasta | |
| Submitted job 12 with external jobid 'Submitted batch job 359401'. | |
| [Sun May 1 12:03:50 2022] | |
| rule sanitize_metadata: | |
| input: data/africa_from_september.tsv | |
| output: results/sanitized_metadata_africa_recent.tsv.xz | |
| log: logs/sanitize_metadata_africa_recent.txt | |
| jobid: 15 | |
| benchmark: benchmarks/sanitize_metadata_africa_recent.txt | |
| wildcards: origin=africa_recent | |
| resources: tmpdir=/tmp, mem_mb=2000 | |
| python3 scripts/sanitize_metadata.py --metadata data/africa_from_september.tsv --metadata-id-columns strain name 'Virus name' --database-id-columns 'Accession ID' gisaid_epi_isl genbank_accession --parse-location-field Location --rename-fields 'Virus name=strain' Type=type 'Accession ID=gisaid_epi_isl' 'Collection date=date' 'Additional location information=additional_location_information' 'Sequence length=length' Host=host 'Patient age=patient_age' Gender=sex Clade=GISAID_clade 'Pango lineage=pango_lineage' pangolin_lineage=pango_lineage Lineage=pango_lineage 'Pangolin version=pangolin_version' Variant=variant 'AA Substitutions=aaSubstitutions' 'Submission date=date_submitted' 'Is reference?=is_reference' 'Is complete?=is_complete' 'Is high coverage?=is_high_coverage' 'Is low coverage?=is_low_coverage' N-Content=n_content GC-Content=gc_content --strip-prefixes hCoV-19/ SARS-CoV-2/ --output results/sanitized_metadata_africa_recent.tsv.xz 2>&1 | tee logs/sanitize_metadata_africa_recent.txt | |
| Submitted job 15 with external jobid 'Submitted batch job 359402'. | |
| [Sun May 1 12:04:49 2022] | |
| Finished job 15. | |
| 1 of 123 steps (1%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:04:49 2022] | |
| Job 13: | |
| Combining metadata files results/sanitized_metadata_global-open.tsv.xz results/sanitized_metadata_africa_recent.tsv.xz -> results/combined_metadata.tsv.xz and adding columns to represent origin | |
| python3 scripts/combine_metadata.py --metadata results/sanitized_metadata_global-open.tsv.xz results/sanitized_metadata_africa_recent.tsv.xz --origins global-open africa_recent --output results/combined_metadata.tsv.xz 2>&1 | tee logs/combine_input_metadata.txt | |
| Submitted job 13 with external jobid 'Submitted batch job 359403'. | |
| [Sun May 1 12:05:19 2022] | |
| Finished job 13. | |
| 2 of 123 steps (2%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:05:19 2022] | |
| Job 80: | |
| Subsample all sequences by 'focal' scheme for build 'southern_region_recent' with the following parameters: | |
| - group by: --group-by country year month | |
| - sequences per group: --sequences-per-group 800 | |
| - subsample max sequences: | |
| - min-date: --min-date 2021-08-01 | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "country.isin(['Angola', 'Union of the Comoros', 'Lesotho', 'Mozambique', 'Seychelles', 'Botswana', 'Eswatini', 'Madagascar', 'Malawi', 'Mauritius', 'Namibia', 'South Africa', 'Zambia', 'Zimbabwe'])" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --min-date 2021-08-01 --query "country.isin(['Angola', 'Union of the Comoros', 'Lesotho', 'Mozambique', 'Seychelles', 'Botswana', 'Eswatini', 'Madagascar', 'Malawi', 'Mauritius', 'Namibia', 'South Africa', 'Zambia', 'Zimbabwe'])" --group-by country year month --sequences-per-group 800 --probabilistic-sampling --output-strains results/southern_region_recent/sample-focal.txt 2>&1 | tee logs/subsample_southern_region_recent_focal.txt | |
| Submitted job 80 with external jobid 'Submitted batch job 359404'. | |
| [Sun May 1 12:05:19 2022] | |
| Job 112: | |
| Subsample all sequences by 'focal' scheme for build 'southern_region_only_recent' with the following parameters: | |
| - group by: --group-by country year month | |
| - sequences per group: --sequences-per-group 800 | |
| - subsample max sequences: | |
| - min-date: --min-date 2021-08-01 | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "country.isin(['Angola', 'Union of the Comoros', 'Lesotho', 'Mozambique', 'Seychelles', 'Botswana', 'Eswatini', 'Madagascar', 'Malawi', 'Mauritius', 'Namibia', 'South Africa', 'Zambia', 'Zimbabwe'])" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --min-date 2021-08-01 --query "country.isin(['Angola', 'Union of the Comoros', 'Lesotho', 'Mozambique', 'Seychelles', 'Botswana', 'Eswatini', 'Madagascar', 'Malawi', 'Mauritius', 'Namibia', 'South Africa', 'Zambia', 'Zimbabwe'])" --group-by country year month --sequences-per-group 800 --probabilistic-sampling --output-strains results/southern_region_only_recent/sample-focal.txt 2>&1 | tee logs/subsample_southern_region_only_recent_focal.txt | |
| Submitted job 112 with external jobid 'Submitted batch job 359405'. | |
| [Sun May 1 12:05:19 2022] | |
| Job 16: | |
| Subsample all sequences by 'focal' scheme for build 'africa_recent' with the following parameters: | |
| - group by: --group-by country year month | |
| - sequences per group: --sequences-per-group 800 | |
| - subsample max sequences: | |
| - min-date: --min-date 2021-08-01 | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "region == 'Africa'" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --min-date 2021-08-01 --query "region == 'Africa'" --group-by country year month --sequences-per-group 800 --probabilistic-sampling --output-strains results/africa_recent/sample-focal.txt 2>&1 | tee logs/subsample_africa_recent_focal.txt | |
| Submitted job 16 with external jobid 'Submitted batch job 359406'. | |
| [Sun May 1 12:05:20 2022] | |
| Job 17: | |
| Subsample all sequences by 'contextual' scheme for build 'africa_recent' with the following parameters: | |
| - group by: | |
| - sequences per group: | |
| - subsample max sequences: | |
| - min-date: | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "region != 'Africa'" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --query "region != 'Africa'" --output-strains results/africa_recent/sample-contextual.txt 2>&1 | tee logs/subsample_africa_recent_contextual.txt | |
| Submitted job 17 with external jobid 'Submitted batch job 359407'. | |
| [Sun May 1 12:05:20 2022] | |
| Job 49: | |
| Subsample all sequences by 'focal' scheme for build 'africa_only_recent' with the following parameters: | |
| - group by: --group-by country year month | |
| - sequences per group: --sequences-per-group 800 | |
| - subsample max sequences: | |
| - min-date: --min-date 2021-08-01 | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "region == 'Africa'" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --min-date 2021-08-01 --query "region == 'Africa'" --group-by country year month --sequences-per-group 800 --probabilistic-sampling --output-strains results/africa_only_recent/sample-focal.txt 2>&1 | tee logs/subsample_africa_only_recent_focal.txt | |
| Submitted job 49 with external jobid 'Submitted batch job 359408'. | |
| [Sun May 1 12:05:20 2022] | |
| Job 81: | |
| Subsample all sequences by 'contextual' scheme for build 'southern_region_recent' with the following parameters: | |
| - group by: | |
| - sequences per group: | |
| - subsample max sequences: | |
| - min-date: | |
| - max-date: | |
| - | |
| - exclude: | |
| - include: | |
| - query: --query "region != 'Africa'" | |
| - priority: | |
| augur filter --metadata results/combined_metadata.tsv.xz --include defaults/include.txt --exclude defaults/exclude.txt --query "region != 'Africa'" --output-strains results/southern_region_recent/sample-contextual.txt 2>&1 | tee logs/subsample_southern_region_recent_contextual.txt | |
| Submitted job 81 with external jobid 'Submitted batch job 359409'. | |
| [Sun May 1 12:05:40 2022] | |
| Finished job 17. | |
| 3 of 123 steps (2%) done | |
| [Sun May 1 12:05:40 2022] | |
| Finished job 81. | |
| 4 of 123 steps (3%) done | |
| [Sun May 1 12:05:50 2022] | |
| Finished job 80. | |
| 5 of 123 steps (4%) done | |
| [Sun May 1 12:05:50 2022] | |
| Finished job 49. | |
| 6 of 123 steps (5%) done | |
| [Sun May 1 12:06:00 2022] | |
| Finished job 16. | |
| 7 of 123 steps (6%) done | |
| [Sun May 1 12:06:10 2022] | |
| Finished job 112. | |
| 8 of 123 steps (7%) done | |
| [Sun May 1 12:13:54 2022] | |
| Finished job 12. | |
| 9 of 123 steps (7%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:13:54 2022] | |
| Job 11: | |
| Combine and deduplicate aligned FASTAs from multiple origins in preparation for subsampling. | |
| python3 scripts/sanitize_sequences.py --sequences data/global_aligned.fasta.xz results/aligned_africa_recent.fasta.xz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout | xz -c -2 > results/combined_sequences_for_subsampling.fasta.xz | |
| Submitted job 11 with external jobid 'Submitted batch job 359410'. | |
| [Sun May 1 12:14:44 2022] | |
| Finished job 11. | |
| 10 of 123 steps (8%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:14:44 2022] | |
| Job 48: | |
| Combine and deduplicate FASTAs | |
| augur filter --sequences results/combined_sequences_for_subsampling.fasta.xz --metadata results/combined_metadata.tsv.xz --exclude-all --include results/africa_only_recent/sample-focal.txt --output-sequences results/africa_only_recent/africa_only_recent_subsampled_sequences.fasta.xz --output-metadata results/africa_only_recent/africa_only_recent_subsampled_metadata.tsv.xz 2>&1 | tee logs/subsample_regions_africa_only_recent.txt | |
| Submitted job 48 with external jobid 'Submitted batch job 359411'. | |
| [Sun May 1 12:14:44 2022] | |
| Job 111: | |
| Combine and deduplicate FASTAs | |
| augur filter --sequences results/combined_sequences_for_subsampling.fasta.xz --metadata results/combined_metadata.tsv.xz --exclude-all --include results/southern_region_only_recent/sample-focal.txt --output-sequences results/southern_region_only_recent/southern_region_only_recent_subsampled_sequences.fasta.xz --output-metadata results/southern_region_only_recent/southern_region_only_recent_subsampled_metadata.tsv.xz 2>&1 | tee logs/subsample_regions_southern_region_only_recent.txt | |
| Submitted job 111 with external jobid 'Submitted batch job 359412'. | |
| [Sun May 1 12:14:44 2022] | |
| Job 79: | |
| Combine and deduplicate FASTAs | |
| augur filter --sequences results/combined_sequences_for_subsampling.fasta.xz --metadata results/combined_metadata.tsv.xz --exclude-all --include results/southern_region_recent/sample-focal.txt results/southern_region_recent/sample-contextual.txt --output-sequences results/southern_region_recent/southern_region_recent_subsampled_sequences.fasta.xz --output-metadata results/southern_region_recent/southern_region_recent_subsampled_metadata.tsv.xz 2>&1 | tee logs/subsample_regions_southern_region_recent.txt | |
| Submitted job 79 with external jobid 'Submitted batch job 359413'. | |
| [Sun May 1 12:14:45 2022] | |
| Job 10: | |
| Combine and deduplicate FASTAs | |
| augur filter --sequences results/combined_sequences_for_subsampling.fasta.xz --metadata results/combined_metadata.tsv.xz --exclude-all --include results/africa_recent/sample-focal.txt results/africa_recent/sample-contextual.txt --output-sequences results/africa_recent/africa_recent_subsampled_sequences.fasta.xz --output-metadata results/africa_recent/africa_recent_subsampled_metadata.tsv.xz 2>&1 | tee logs/subsample_regions_africa_recent.txt | |
| Submitted job 10 with external jobid 'Submitted batch job 359414'. | |
| [Sun May 1 12:16:14 2022] | |
| Finished job 111. | |
| 11 of 123 steps (9%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:16:14 2022] | |
| Finished job 79. | |
| 12 of 123 steps (10%) done | |
| [Sun May 1 12:16:14 2022] | |
| Job 110: | |
| Running nextclade QC and aligning sequences to defaults/reference_seq.fasta | |
| - gaps relative to reference are considered real | |
| python3 scripts/sanitize_sequences.py --sequences results/southern_region_only_recent/southern_region_only_recent_subsampled_sequences.fasta.xz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_before_nextclade_southern_region_only_recent.txt | nextclade run --jobs 8 --input-fasta /dev/stdin --reference defaults/reference_seq.fasta --input-dataset data/sars-cov-2-nextclade-defaults --output-tsv results/southern_region_only_recent/nextclade_qc.tsv --output-dir results/southern_region_only_recent/translations --output-basename aligned --output-fasta results/southern_region_only_recent/aligned.fasta --output-insertions results/southern_region_only_recent/insertions.tsv 2>&1 | tee logs/align_southern_region_only_recent.txt | |
| Submitted job 110 with external jobid 'Submitted batch job 359415'. | |
| Select jobs to execute... | |
| [Sun May 1 12:16:16 2022] | |
| Job 78: | |
| Running nextclade QC and aligning sequences to defaults/reference_seq.fasta | |
| - gaps relative to reference are considered real | |
| python3 scripts/sanitize_sequences.py --sequences results/southern_region_recent/southern_region_recent_subsampled_sequences.fasta.xz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_before_nextclade_southern_region_recent.txt | nextclade run --jobs 8 --input-fasta /dev/stdin --reference defaults/reference_seq.fasta --input-dataset data/sars-cov-2-nextclade-defaults --output-tsv results/southern_region_recent/nextclade_qc.tsv --output-dir results/southern_region_recent/translations --output-basename aligned --output-fasta results/southern_region_recent/aligned.fasta --output-insertions results/southern_region_recent/insertions.tsv 2>&1 | tee logs/align_southern_region_recent.txt | |
| Submitted job 78 with external jobid 'Submitted batch job 359416'. | |
| [Sun May 1 12:16:55 2022] | |
| Finished job 10. | |
| 13 of 123 steps (11%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:16:55 2022] | |
| Job 9: | |
| Running nextclade QC and aligning sequences to defaults/reference_seq.fasta | |
| - gaps relative to reference are considered real | |
| python3 scripts/sanitize_sequences.py --sequences results/africa_recent/africa_recent_subsampled_sequences.fasta.xz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_before_nextclade_africa_recent.txt | nextclade run --jobs 8 --input-fasta /dev/stdin --reference defaults/reference_seq.fasta --input-dataset data/sars-cov-2-nextclade-defaults --output-tsv results/africa_recent/nextclade_qc.tsv --output-dir results/africa_recent/translations --output-basename aligned --output-fasta results/africa_recent/aligned.fasta --output-insertions results/africa_recent/insertions.tsv 2>&1 | tee logs/align_africa_recent.txt | |
| Submitted job 9 with external jobid 'Submitted batch job 359417'. | |
| [Sun May 1 12:17:15 2022] | |
| Finished job 48. | |
| 14 of 123 steps (11%) done | |
| Select jobs to execute... | |
| [Sun May 1 12:17:15 2022] | |
| Job 47: | |
| Running nextclade QC and aligning sequences to defaults/reference_seq.fasta | |
| - gaps relative to reference are considered real | |
| python3 scripts/sanitize_sequences.py --sequences results/africa_only_recent/africa_only_recent_subsampled_sequences.fasta.xz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_before_nextclade_africa_only_recent.txt | nextclade run --jobs 8 --input-fasta /dev/stdin --reference defaults/reference_seq.fasta --input-dataset data/sars-cov-2-nextclade-defaults --output-tsv results/africa_only_recent/nextclade_qc.tsv --output-dir results/africa_only_recent/translations --output-basename aligned --output-fasta results/africa_only_recent/aligned.fasta --output-insertions results/africa_only_recent/insertions.tsv 2>&1 | tee logs/align_africa_only_recent.txt | |
| Submitted job 47 with external jobid 'Submitted batch job 359418'. | |
| [Sun May 1 13:01:59 2022] | |
| Finished job 78. | |
| 15 of 123 steps (12%) done | |
| Select jobs to execute... | |
| [Sun May 1 13:01:59 2022] | |
| rule join_metadata_and_nextclade_qc: | |
| input: results/southern_region_recent/southern_region_recent_subsampled_metadata.tsv.xz, results/southern_region_recent/nextclade_qc.tsv | |
| output: results/southern_region_recent/metadata_with_nextclade_qc.tsv | |
| log: logs/join_metadata_and_nextclade_qc_southern_region_recent.txt | |
| jobid: 83 | |
| benchmark: benchmarks/join_metadata_and_nextclade_qc_southern_region_recent.txt | |
| wildcards: build_name=southern_region_recent | |
| resources: tmpdir=/tmp | |
| python3 scripts/join-metadata-and-clades.py results/southern_region_recent/southern_region_recent_subsampled_metadata.tsv.xz results/southern_region_recent/nextclade_qc.tsv -o results/southern_region_recent/metadata_with_nextclade_qc.tsv 2>&1 | tee logs/join_metadata_and_nextclade_qc_southern_region_recent.txt | |
| Submitted job 83 with external jobid 'Submitted batch job 359420'. | |
| [Sun May 1 13:01:59 2022] | |
| Job 77: | |
| Mask bases in alignment results/southern_region_recent/aligned.fasta | |
| - masking 100 from beginning | |
| - masking 200 from end | |
| - masking other sites: 21987 21846 | |
| python3 scripts/mask-alignment.py --alignment results/southern_region_recent/aligned.fasta --mask-from-beginning 100 --mask-from-end 200 --mask-sites 21987 21846 --mask-terminal-gaps --output results/southern_region_recent/masked.fasta 2> logs/mask_southern_region_recent.txt | |
| Submitted job 77 with external jobid 'Submitted batch job 359421'. | |
| [Sun May 1 13:02:29 2022] | |
| Error in rule join_metadata_and_nextclade_qc: | |
| jobid: 83 | |
| output: results/southern_region_recent/metadata_with_nextclade_qc.tsv | |
| log: logs/join_metadata_and_nextclade_qc_southern_region_recent.txt (check log file(s) for error message) | |
| shell: | |
| python3 scripts/join-metadata-and-clades.py results/southern_region_recent/southern_region_recent_subsampled_metadata.tsv.xz results/southern_region_recent/nextclade_qc.tsv -o results/southern_region_recent/metadata_with_nextclade_qc.tsv 2>&1 | tee logs/join_metadata_and_nextclade_qc_southern_region_recent.txt | |
| (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) | |
| cluster_jobid: Submitted batch job 359420 | |
| Logfile logs/join_metadata_and_nextclade_qc_southern_region_recent.txt: | |
| Traceback (most recent call last): | |
| File "/usr/people/pvh/miniconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc | |
| return self._engine.get_loc(casted_key) | |
| File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc | |
| File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc | |
| File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item | |
| File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item | |
| KeyError: 'Nextclade_pango' | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "scripts/join-metadata-and-clades.py", line 150, in <module> | |
| main() | |
| File "scripts/join-metadata-and-clades.py", line 140, in main | |
| result[col] = result[col].fillna(VALUE_MISSING_DATA) | |
| File "/usr/people/pvh/miniconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/frame.py", line 3505, in __getitem__ | |
| indexer = self.columns.get_loc(key) | |
| File "/usr/people/pvh/miniconda3/envs/nextstrain/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc | |
| raise KeyError(key) from err | |
| KeyError: 'Nextclade_pango' | |
| Error executing rule join_metadata_and_nextclade_qc on cluster (jobid: 83, external: Submitted batch job 359420, jobscript: /usr/people/pvh/ncov/.snakemake/tmp.8yp8bknw/join_metadata_and_nextclade_qc.83.sh). For error details see the cluster log and the log files of the involved rule(s). | |
| [Sun May 1 13:02:54 2022] | |
| Finished job 77. | |
| 16 of 123 steps (13%) done | |
| [Sun May 1 13:11:26 2022] | |
| Finished job 110. | |
| 17 of 123 steps (14%) done | |
| [Sun May 1 13:35:17 2022] | |
| Finished job 9. | |
| 18 of 123 steps (15%) done | |
| [Sun May 1 13:55:29 2022] | |
| Finished job 47. | |
| 19 of 123 steps (15%) done | |
| Shutting down, this might take some time. | |
| Exiting because a job execution failed. Look above for error message | |
| Complete log: /usr/people/pvh/ncov/.snakemake/log/2022-05-01T120348.527600.snakemake.log |
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