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nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing
https://nf-co.re/pathogensurveillance
MIT License
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PATHOGENSURVEILLANCE:RECORD_MESSAGES process not finished but pipeline says it completed successfully #59

Closed masudermann closed 6 months ago

masudermann commented 7 months ago

Description of the bug

I haven't seen this before, but with the following dataset: mixed_bacteria.csv, I am not getting a RECORD_MESSAGES directory when I run the pipeline using the following command:

nextflow run main.nf --input /home/marthasudermann/pathogensurveillance/test/data/metadata/mixed_bacteria.csv --outdir test_mixedbacteria --bakta_db /home/marthasudermann/Software/bakta_db_02_2024/db/ -profile docker -resume

Every process finishes as expected but I am not getting any output when it comes time to compile error messages. Because of this, I don't get the expected PREPARE_REPORT_INPUT directory nor the MAIN_REPORT directory.

After encountering this bug, I made sure to pull any recent changes and reran the xan test dataset. It ran fully and the final report rendered. I then tried to rerun mixed dataset (after removing work directory), and still didn't get the final expected outputs.

Command used and terminal output


nextflow run main.nf --input /home/marthasudermann/pathogensurveillance/test/data/metadata/mixed_bacteria.csv --outdir test_mixedbacteria --bakta_db /home/marthasudermann/Software/bakta_db_02_2024/db/ -profile docker -resume

#Final snippet of output
[8f/0e1fed] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_MARKDUPLICATES (GCF_017189435_1_SAMN11100994)         [100%] 30 of 30 ✔
[dd/40aacd] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_SORTSAM_2 (GCF_017189435_1_SAMN11100994)              [100%] 30 of 30 ✔
[b9/b3cd7f] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:SAMTOOLS_INDEX (GCF_017189435_1_SAMN11100994)                [100%] 30 of 30 ✔
[64/9f3b86] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:MAKE_REGION_FILE (all_GCF_017189435_1)                     [100%] 3 of 3 ✔
[0f/839051] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GRAPHTYPER_GENOTYPE (all_GCF_003097195_1)                  [100%] 3 of 3 ✔
[be/0b9c75] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GRAPHTYPER_VCFCONCATENATE (all_GCF_003097195_1)            [100%] 3 of 3 ✔
[df/ba4f72] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:TABIX_TABIX (all_GCF_003097195_1)                          [100%] 3 of 3 ✔
[ff/b28e4c] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:BGZIP_MAKE_GZIP (all_GCF_003097195_1)                      [100%] 3 of 3 ✔
[04/f616e0] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GATK4_VARIANTFILTRATION (all_GCF_003097195_1)              [100%] 3 of 3 ✔
[07/923c77] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:VCFLIB_VCFFILTER (all_GCF_003097195_1)                     [100%] 3 of 3 ✔
[56/4589c7] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:VCF_TO_TAB (all_GCF_003097195_1)                                         [100%] 3 of 3 ✔
[2b/1ab0a5] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:VCF_TO_SNPALN (all_GCF_003097195_1)                                      [100%] 3 of 3 ✔
[a7/6bcee3] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:IQTREE2_SNP (all_GCF_003097195_1)                                        [100%] 3 of 3 ✔
[56/7c6bf9] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:SUBSET_READS (SAMN11100995)                                               [100%] 30 of 30 ✔
[cd/830952] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FASTP (SAMN11100994)                                                      [100%] 30 of 30 ✔
[98/640a08] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:SPADES (SAMN11100994)                                                     [100%] 30 of 30 ✔
[ae/19cfc1] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FILTER_ASSEMBLY (SAMN11100994)                                            [100%] 30 of 30 ✔
[d1/15cf1d] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:QUAST (GCF_017189435_1)                                                   [100%] 3 of 3 ✔
[38/6ecaa7] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:BAKTA_BAKTA (SAMN11100994)                                                [100%] 30 of 30 ✔
[c2/21abb4] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:PIRATE (all)                                                        [100%] 1 of 1 ✔
[49/5a3382] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:REFORMAT_PIRATE_RESULTS (all)                                       [100%] 1 of 1 ✔
[a6/035430] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:CALCULATE_POCP (all)                                                [100%] 1 of 1 ✔
[b2/a01bec] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ALIGN_FEATURE_SEQUENCES (all)                                       [100%] 1 of 1 ✔
[d6/78297f] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:RENAME_CORE_GENE_HEADERS (all)                                      [100%] 1 of 1 ✔
[46/d6c2bb] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:SUBSET_CORE_GENES (all)                                             [100%] 1 of 1 ✔
[d4/fd3e63] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:MAFFT_SMALL (all)                                                   [100%] 29 of 29 ✔
[6b/2236e8] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:IQTREE2_CORE (all)                                                  [100%] 1 of 1 ✔
[b0/0b4ac4] process > PATHOGENSURVEILLANCE:CUSTOM_DUMPSOFTWAREVERSIONS (1)                                                           [100%] 1 of 1 ✔
[77/71740a] process > PATHOGENSURVEILLANCE:MULTIQC                                                                                   [100%] 1 of 1 ✔
[-        ] process > PATHOGENSURVEILLANCE:RECORD_MESSAGES                                                                           -
[-        ] process > PATHOGENSURVEILLANCE:PREPARE_REPORT_INPUT                                                                      -
[-        ] process > PATHOGENSURVEILLANCE:MAIN_REPORT                                                                               -
-[nf-core/plantpathsurveil] Pipeline completed successfully-
Completed at: 15-Apr-2024 14:10:22
Duration    : 4h 1m 33s
CPU hours   : 49.0
Succeeded   : 924

Relevant files

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System information

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masudermann commented 6 months ago

It seems that Zach was able to resolve this issue, and I was able to rerun the pipeline after pulling recent changes and get the necessary output directories.