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Summary report fails as multiqc doesn't generate SVG files. #824

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nagendraKU opened this issue Jan 13, 2025 · 1 comment
Open

Summary report fails as multiqc doesn't generate SVG files. #824

nagendraKU opened this issue Jan 13, 2025 · 1 comment
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bug Something isn't working

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@nagendraKU
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Description of the bug

Running the test profile fails at the Summary report stage because Multiqc doesn't generate SVG file for fastqc_per_sequence_quality_scores_plot.svg. I checked the results/multiqc/multiqc_data folder and the fastqc_per_sequence_quality_scores_plot.txt data file is present. The multiqc_plots folder is empty in all its subfolders (svg, pdf, png).

Run log summary:

NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv) COMPLETED  0
NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE (Metadata.tsv) COMPLETED     0
NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1a) COMPLETED  0
NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a) COMPLETED  0
NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_1a) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1a) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_2a) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_2a) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_1)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC (sampleID_2)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:FASTQC (sampleID_2) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME   COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD (cutadapt_standard)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 (FW)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1 (RV)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE (cutadapt_standard_summary.tsv)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN (FW) COMPLETED    0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN (RV) COMPLETED    0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:CUTADAPT_TAXONOMY (assignTaxonomy)   COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (sampleID_1a)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (sampleID_1)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (sampleID_2)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM (sampleID_2a)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN (GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 (RV)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2 (FW)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:VSEARCH_CLUSTER (ASV_post_clustering)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:FILTER_CLUSTERS (ASV_post_clustering)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP (ASV_post_clustering_filtered.fna)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU (ASV_post_clustering_filtered.fna)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV (ASV_seqs.ssu.fasta) COMPLETED  0
NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ (ASV_seqs.len.fasta)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV (ASV_table.len.tsv) COMPLETED     0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ (ASV_seqs.len.fasta) COMPLETED    0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY (ASV_seqs.len.fasta,assignTaxonomy.trim.fastq.gz)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY (rep-seqs.qza,GTGYCAGCMGCCGCGGTAA-GGACTACNVGGGTWTCTAAT-classifier.qza) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_ADDSPECIES (ASV_tax.rds,addSpecies.fna)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_INTAX_QIIME2 (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX (ASV_tax_species.gtdb_R07-RS207.tsv)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE (ASV_tax_species.gtdb_R07-RS207.tsv)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT (ASV_table.len.tsv,ASV_tax_species.gtdb_R07-RS207.tsv,Metadata.tsv) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TABLEFILTERTAXA (taxa:mitochondria,chloroplast;min-freq:10;min-samples:2)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ_INASV COMPLETED     0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_SEQFILTERTABLE (rep-seqs.qza-filter-by-filtered-table.qza)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_TAX (filtered-table-treatment1-2) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_TAX (filtered-table-treatment1-3) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM (mix8) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM (badpairwise10)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM (treatment1)   COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_TAX (filtered-table-treatment1-4) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:ANCOMBC_FORMULA_ASV (filtered-table-treatment1)   COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT (1) COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA (1) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG (rel-table-ASV.tsv)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ (qiime2) COMPLETED  0
NFCORE_AMPLISEQ:AMPLISEQ:PHYLOSEQ_WORKFLOW:PHYLOSEQ (dada2) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE   COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (mix8--2)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_ASV (mix8-)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (mix8--4)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (mix8--3)      COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (badpairwise10--2)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (badpairwise10--4)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_ASV (badpairwise10-)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (badpairwise10--3)     COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--3)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--2)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--4)        COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_ASV (treatment1-)  COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP (badpairwise10)    COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP (treatment1)       COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2 (1) COMPLETED       0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2 COMPLETED    0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG (1) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG (2) COMPLETED   0
NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC COMPLETED 0
NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1) FAILED 1

Command used and terminal output

Command used:
$ nextflow run nf-core/ampliseq -r 2.12.0 -profile test,singularity --outdir testresults --skip_alpha_rarefaction --skip_diversity_indices

Output

Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)` terminated with an error exit status (1)


Command executed:

  \#!/usr/bin/env Rscript
  library(rmarkdown)

 \# Work around  https://github.com/rstudio/rmarkdown/issues/1508
  \# If the symbolic link is not replaced by a physical file
  \# output- and temporary files will be written to the original directory.
  file.copy("./report_template.Rmd", "./template.Rmd", overwrite = TRUE)

  rmarkdown::render("template.Rmd", output_file = "summary_report.html", params = list(css='nf-core_style.css',report_logo='nf-core-ampliseq_logo_light_long.png',workflow_manifest_version='2.12.0',workflow_scriptid='bf04a499cc',report_title='Summary of analysis results',metadata='Metadata.tsv',input_samplesheet='Samplesheet.tsv',mqc_plot='multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg',cutadapt_summary='cutadapt_summary.tsv',trunc_qmin=25,trunc_rmin=0.75,trunclenf='null',trunclenr='null',max_ee=2,dada_qc_f_path='FW_qual_stats.svg',dada_qc_r_path='RV_qual_stats.svg',dada_pp_qc_f_path='FW_preprocessed_qual_stats.svg',dada_pp_qc_r_path='RV_preprocessed_qual_stats.svg',dada_filtntrim_args='filterAndTrim.args.txt',dada_sample_inference='independent',dada_err_path='1_1.err.svg,1_2.err.svg',dada_err_run='1',asv_table_path='ASV_table.tsv',path_asv_fa='ASV_post_clustering_filtered.fna',path_dada2_tab='DADA2_table.tsv',dada_stats_path='DADA2_stats.tsv',vsearch_cluster='ASV_post_clustering_filtered.table.tsv',vsearch_cluster_id='0.97',path_barrnap_sum='summary.tsv',filter_ssu_stats='stats.ssu.tsv',filter_ssu_asv='ASV_seqs.ssu.fasta',filter_ssu='bac',filter_len_asv='stats.len.tsv',filter_len_asv_len_orig='ASV_len_orig.tsv',min_len_asv=0,max_len_asv=255,dada2_taxonomy='ASV_tax_species.gtdb_R07-RS207.tsv',dada2_ref_tax_title='GTDB - Genome Taxonomy Database - Release R07-RS207',dada2_ref_tax_file='[https://data.gtdb.ecogenomic.org/releases/release207/207.0/genomic_files_reps/bac120_ssu_reps_r207.tar.gz, https://data.gtdb.ecogenomic.org/releases/release207/207.0/genomic_files_reps/ar53_ssu_reps_r207.tar.gz]',dada2_ref_tax_citation='Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27. PMID: 30148503.',cut_dada_ref_taxonomy='assignTaxonomy.cutadapt.log',qiime2_taxonomy='taxonomy.tsv',qiime2_ref_tax_title='Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only',qiime2_ref_tax_file='[https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta, https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt]',qiime2_ref_tax_citation='McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610�618 (2012). https://doi.org/10.1038/ismej.2011.139',val_used_taxonomy='DADA2',filter_stats_tsv='count_table_filter_stats.tsv',qiime2_filtertaxa='245,42',exclude_taxa='mitochondria,chloroplast',min_frequency='10',min_samples='2',barplot=TRUE,metadata_category_barplot='treatment1,badpairwise10',abundance_tables=TRUE,ancombc='ancombc/da_barplot/Category-mix8-ASV,ancombc/da_barplot/Category-mix8-level-2,ancombc/da_barplot/Category-mix8-level-4,ancombc/da_barplot/Category-mix8-level-3,ancombc/da_barplot/Category-badpairwise10-level-2,ancombc/da_barplot/Category-badpairwise10-level-4,ancombc/da_barplot/Category-badpairwise10-ASV,ancombc/da_barplot/Category-badpairwise10-level-3,ancombc/da_barplot/Category-treatment1-level-3,ancombc/da_barplot/Category-treatment1-level-2,ancombc/da_barplot/Category-treatment1-level-4,ancombc/da_barplot/Category-treatment1-ASV',ancombc_formula='ancombc_formula/da_barplot/Category-treatment1-level-2,ancombc_formula/da_barplot/Category-treatment1-level-3,ancombc_formula/da_barplot/Category-treatment1-ASV,ancombc_formula/da_barplot/Category-treatment1-level-4',sbdi='sbdi/annotation.tsv,sbdi/asv-table.tsv,sbdi/dna.tsv,sbdi/emof.tsv,sbdi/event.tsv',phyloseq='phyloseq/qiime2_phyloseq.rds,phyloseq/dada2_phyloseq.rds'), envir = new.env())

  writeLines(c("\"NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT\":",
      paste0("    R: ", paste0(R.Version()[c("major","minor")], collapse = ".")),
      paste0("    rmarkdown: ", packageVersion("rmarkdown")),
      paste0("    knitr: ", packageVersion("knitr")) ),
      "versions.yml")

Command exit status:
  1

Command output:
  [1] TRUE
  1/156
  2/156 [libraries]
  3/156
  4/156 [setup]
  5/156
  6/156 [unnamed-chunk-1]
  7/156
  8/156 [unnamed-chunk-2]
  9/156
  10/156 [unnamed-chunk-3]
  11/156
  12/156 [unnamed-chunk-4]
  13/156
  14/156 [unnamed-chunk-5]
  15/156
  16/156 [unnamed-chunk-6]
  17/156
  18/156 [unnamed-chunk-7]
  19/156
  20/156 [unnamed-chunk-8]

Command error:
  [1] TRUE


  processing file: template.Rmd
  1/156
  2/156 [libraries]
  3/156
  4/156 [setup]
  5/156
  6/156 [unnamed-chunk-1]
  7/156
  8/156 [unnamed-chunk-2]
  9/156
  10/156 [unnamed-chunk-3]
  11/156
  12/156 [unnamed-chunk-4]
  13/156
  14/156 [unnamed-chunk-5]
  15/156
  16/156 [unnamed-chunk-6]
  17/156
  18/156 [unnamed-chunk-7]
  19/156
  20/156 [unnamed-chunk-8]

  Quitting from lines 245-246 [unnamed-chunk-8] (template.Rmd)
  Error in `knitr::include_graphics()`:
  ! Cannot find the file(s): "multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg"
  Backtrace:
   1. knitr::include_graphics(params$mqc_plot)
  Execution halted

Relevant files

nextflow.log

System information

Nextflow 24.10.3.5933
ampliseq 2.12.0
Singularity 3.8.7
@nagendraKU nagendraKU added the bug Something isn't working label Jan 13, 2025
@d4straub
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I run the pipeline with NXF_VER=24.10.3 nextflow run nf-core/ampliseq -r 2.12.0 -profile test,singularity --outdir results_test_2.12.0 --skip_alpha_rarefaction --skip_diversity_indices and it worked fine. So the problem seems to be not the pipeline.
I assume some problem with the file system or such. Could you please simply resume the pipeline, i.e. append a -resume to your command?

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@d4straub @nagendraKU