pathogensurveillance.nf error before picard step

[logankblair]

[d7/51c3d1] process > PATHOGENSURVEILLANCE:FASTQC (650670)                                                  [100%] 9 of 9, cached: 9 ✔
[09/65a011] process > PATHOGENSURVEILLANCE:COARSE_SAMPLE_TAXONOMY:BBMAP_SENDSKETCH (650670)                 [100%] 9 of 9, cached: 9 ✔
[90/8b505c] process > PATHOGENSURVEILLANCE:COARSE_SAMPLE_TAXONOMY:INITIAL_CLASSIFICATION (650670)           [100%] 9 of 9, cached: 9 ✔
[74/2c8cce] process > PATHOGENSURVEILLANCE:DOWNLOAD_REFERENCES:FIND_ASSEMBLIES (Mycobacteriaceae)           [100%] 1 of 1, cached: 1 ✔
[08/fb0349] process > PATHOGENSURVEILLANCE:DOWNLOAD_REFERENCES:PICK_ASSEMBLIES (650670)                     [100%] 9 of 9, cached: 9 ✔
[3e/2db235] process > PATHOGENSURVEILLANCE:DOWNLOAD_REFERENCES:DOWNLOAD_ASSEMBLIES (GCF_000332605_1)        [100%] 22 of 22, cached: 22 ✔
[ef/ea91fa] process > PATHOGENSURVEILLANCE:DOWNLOAD_REFERENCES:MAKE_GFF_WITH_FASTA (GCF_000332605_1)        [100%] 22 of 22, cached: 22 ✔
[ce/20e9a9] process > PATHOGENSURVEILLANCE:DOWNLOAD_REFERENCES:SOURMASH_SKETCH_GENOME (GCF_000332605_1)     [100%] 22 of 22, cached: 22 ✔
[ae/a29722] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:SUBSET_READS (194149)                          [100%] 9 of 9, cached: 9 ✔
[51/d56f1c] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:KHMER_TRIMLOWABUND (194148)                    [100%] 9 of 9, cached: 9 ✔
[9c/943f31] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:SOURMASH_SKETCH_READS (194148)                 [100%] 9 of 9, cached: 9 ✔
[-        ] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:SOURMASH_SKETCH_GENOME                         -
[27/d5bc74] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:SOURMASH_COMPARE (all)                         [100%] 1 of 1, cached: 1 ✔
[9e/df7112] process > PATHOGENSURVEILLANCE:ASSIGN_REFERENCES:ASSIGN_GROUP_REFERENCES (all)                  [100%] 1 of 1, cached: 1 ✔
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:REFERENCE_INDEX:PICARD_CREATESEQUENCEDICTIONARY -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:REFERENCE_INDEX:SAMTOOLS_FAIDX                  -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:REFERENCE_INDEX:BWA_INDEX                       -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:CALCULATE_DEPTH                     -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:SUBSET_READS                        -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:BWA_MEM                             -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_ADDORREPLACEREADGROUPS       -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_SORTSAM_1                    -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_MARKDUPLICATES               -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:PICARD_SORTSAM_2                    -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:SAMTOOLS_INDEX                      -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:MAKE_REGION_FILE                  -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GRAPHTYPER_GENOTYPE               -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GRAPHTYPER_VCFCONCATENATE         -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:TABIX_TABIX                       -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:BGZIP_MAKE_GZIP                   -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:GATK4_VARIANTFILTRATION           -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:CALL_VARIANTS:VCFLIB_VCFFILTER                  -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:VCF_TO_TAB                                      -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:VCF_TO_SNPALN                                   -
[-        ] process > PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:IQTREE2_SNP                                     -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:SUBSET_READS                                     -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FASTP                                            -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:SPADES                                           -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:FILTER_ASSEMBLY                                  -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:QUAST                                            -
[-        ] process > PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:BAKTA_BAKTA                                      -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:PIRATE                                     -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:REFORMAT_PIRATE_RESULTS                    -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:CALCULATE_POCP                             -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:ALIGN_FEATURE_SEQUENCES                    -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:RENAME_CORE_GENE_HEADERS                   -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:SUBSET_CORE_GENES                          -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:MAFFT_SMALL                                -
[-        ] process > PATHOGENSURVEILLANCE:CORE_GENOME_PHYLOGENY:IQTREE2_CORE                               -
[-        ] process > PATHOGENSURVEILLANCE:CUSTOM_DUMPSOFTWAREVERSIONS                                      -
[-        ] process > PATHOGENSURVEILLANCE:MULTIQC                                                          -
[d5/c6f0ba] process > PATHOGENSURVEILLANCE:RECORD_MESSAGES (All)                                            [100%] 1 of 1, cached: 1 ✔
[-        ] process > PATHOGENSURVEILLANCE:PREPARE_REPORT_INPUT                                             -
[-        ] process > PATHOGENSURVEILLANCE:MAIN_REPORT                                                      -
ERROR ~ toIndex = 12

 -- Check script './workflows/pathogensurveillance.nf' at line: 263 or see '.nextflow.log' file for more details

[zachary-foster]

What dataset produced this error?

[logankblair]

This was a custom dataset I was testing. The input looks like:
`

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Shortread_1	Shortread_2	color_by	patient
/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194148_1.fastq.gz	/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194148_2.fastq.gz	patient	1
/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194149_1.fastq.gz	/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194149_2.fastq.gz	patient	1
/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194152_1.fastq.gz	/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194152_2.fastq.gz	patient	3
/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194153_1.fastq.gz	/home/buchananr/Desktop/pathogensurveillance/test_reads/ERR11194153_2.fastq.gz	patient	3

`

[logankblair]

It might have been fixed by the changes to assign_group_reference.R, because it looks like that output was all NAs and null
Need to test this still.

[logankblair]

This step ran successfully after changes to assign_group_reference.R