Running PHoeNIx

You should have already set up your config file to make sure Nextflow knows how to run the programs within PHoeNIx. If you haven't already, please review the config set up portion of the install page.

Inputs

PHoeNIx currently only runs on Illumina paired-end reads. Multiple samples can be run using a samplesheet.csv file

nextflow run CDCgov/phoenix -profile <docker/singularity/custom> --input samplesheet.csv

Samplesheet Input

You will need to create a samplesheet with information about the samples you would like to analyze before running the pipeline. Use the --input parameter to specify its location. It must be a comma-separated file (csv) with at least 3 columns and a header row, as shown in the example below. DO NOT HAVE ANY SPACES IN THIS FILE. Do make sure the paths are full paths and not relative. For best results use the automated samplesheet creation scripts described in the automated section below.

--input '[path to samplesheet file]'

Full Samplesheet

The samplesheet can have as many columns as you desire; however, there is a strict requirement for the first 3 columns to match those defined in the table below.

A final samplesheet file consisting of paired-end data may look something like the one below.

sample,fastq_1,fastq_2
SAMPLE_1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
SAMPLE_2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
SAMPLE_3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz

Column	Description
sample	Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (_).
fastq_1	Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".
fastq_2	Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".

An example samplesheet has been provided with the pipeline and can be used for testing.

Samplesheet Creation - Automated

A script is available to create a samplesheet from a directory of fastq files. The script will search 1 directory deep and attempt to determine sample id names and pairing/multilane information and will automatically create a samplesheet.

- Please review the samplesheet for accuracy before using it in the pipeline.

phoenix/bin/create_samplesheet.sh <directory of fastq files> > samplesheet.csv

You can change the name of the samplesheet.csv above to anything you want.

Outputs

The output of PHoeNIx is structured like the following:

📦results ┣ 📂SRR13183128 ┃ ┣ 📂ANI ┃ ┃ ┣ 📂fastANI ┃ ┃ ┃ ┗ 📜SRR13183128.fastANI.txt ┃ ┃ ┣ 📂mash_dist ┃ ┃ ┃ ┣ 📜SRR13183128.txt ┃ ┃ ┃ ┗ 📜SRR13183128_best_MASH_hits.txt ┃ ┃ ┗ 📜SRR13183128.ani.txt ┃ ┣ 📂Assembly ┃ ┃ ┣ 📜SRR13183128.assembly.gfa.gz ┃ ┃ ┣ 📜SRR13183128.bbmap_filtered.log ┃ ┃ ┣ 📜SRR13183128.contigs.fa.gz ┃ ┃ ┣ 📜SRR13183128.filtered.scaffolds.fa.gz ┃ ┃ ┣ 📜SRR13183128.scaffolds.fa.gz ┃ ┃ ┣ 📜SRR13183128.spades.log ┃ ┃ ┗ 📜warnings.log ┃ ┣ 📂BUSCO ┃ ┃ ┣ 📜SRR13183128-auto-busco.batch_summary.txt ┃ ┃ ┣ 📜short_summary.generic.bacteria_odb10.SRR13183128.scaffolds.fa.json ┃ ┃ ┣ 📜short_summary.generic.bacteria_odb10.SRR13183128.scaffolds.fa.txt ┃ ┃ ┣ 📜short_summary.specific.enterobacterales_odb10.SRR13183128.scaffolds.fa.json ┃ ┃ ┗ 📜short_summary.specific.enterobacterales_odb10.SRR13183128.scaffolds.fa.txt ┃ ┣ 📂fastp_singles ┃ ┃ ┣ 📜SRR13183128_singles.fastp.html ┃ ┃ ┗ 📜SRR13183128_singles.fastp.json ┃ ┣ 📂fastp_trimd ┃ ┃ ┣ 📜SRR13183128.fastp.html ┃ ┃ ┣ 📜SRR13183128.fastp.json ┃ ┃ ┣ 📜SRR13183128_1.fail.fastq.gz ┃ ┃ ┣ 📜SRR13183128_1.trim.fastq.gz ┃ ┃ ┣ 📜SRR13183128_2.fail.fastq.gz ┃ ┃ ┣ 📜SRR13183128_2.trim.fastq.gz ┃ ┃ ┣ 📜SRR13183128_raw_read_counts.txt ┃ ┃ ┗ 📜SRR13183128_trimmed_read_counts.txt ┃ ┣ 📂fastqc_stats ┃ ┃ ┣ 📜SRR13183128_1_fastqc.html ┃ ┃ ┣ 📜SRR13183128_1_fastqc.zip ┃ ┃ ┣ 📜SRR13183128_2_fastqc.html ┃ ┃ ┗ 📜SRR13183128_2_fastqc.zip ┃ ┣ 📂gamma_ar ┃ ┃ ┣ 📜SRR13183128_ResGANNCBI_20210507_srst2.gamma ┃ ┃ ┗ 📜SRR13183128_ResGANNCBI_20210507_srst2.psl ┃ ┣ 📂gamma_hv ┃ ┃ ┣ 📜SRR13183128_Hyper_Virulence_20220414.gamma ┃ ┃ ┗ 📜SRR13183128_Hyper_Virulence_20220414.psl ┃ ┣ 📂gamma_pf ┃ ┃ ┣ 📜SRR13183128_PF-Replicons_20220414.gamma ┃ ┃ ┗ 📜SRR13183128_PF-Replicons_20220414.psl ┃ ┣ 📂kraken2_asmbld ┃ ┃ ┣ 📂krona ┃ ┃ ┃ ┗ 📜SRR13183128_asmbld.html ┃ ┃ ┣ 📜SRR13183128.classified.fastq.gz ┃ ┃ ┣ 📜SRR13183128.kraken2_asmbld.classifiedreads.txt ┃ ┃ ┣ 📜SRR13183128.kraken2_asmbld.report.txt ┃ ┃ ┣ 📜SRR13183128.mpa ┃ ┃ ┗ 📜SRR13183128.unclassified.fastq.gz ┃ ┣ 📂kraken2_asmbld_weighted ┃ ┃ ┣ 📂krona ┃ ┃ ┃ ┗ 📜SRR13183128_wtasmbld.html ┃ ┃ ┣ 📜SRR13183128.summary.txt ┃ ┃ ┗ 📜SRR13183128_weighted_report.txt ┃ ┣ 📂kraken2_trimd ┃ ┃ ┣ 📂krona ┃ ┃ ┃ ┗ 📜SRR13183128_trimd.html ┃ ┃ ┣ 📜SRR13183128.classified_1.fastq.gz ┃ ┃ ┣ 📜SRR13183128.classified_2.fastq.gz ┃ ┃ ┣ 📜SRR13183128.kraken2_trimd.classifiedreads.txt ┃ ┃ ┣ 📜SRR13183128.kraken2_trimd.report.txt ┃ ┃ ┣ 📜SRR13183128.mpa ┃ ┃ ┣ 📜SRR13183128.unclassified_1.fastq.gz ┃ ┃ ┗ 📜SRR13183128.unclassified_2.fastq.gz ┃ ┣ 📂mlst ┃ ┃ ┗ 📜SRR13183128.tsv ┃ ┣ 📂quast ┃ ┃ ┗ 📜SRR13183128_report.tsv ┃ ┣ 📂removedAdapters ┃ ┃ ┗ 📜SRR13183128.bbduk.log ┃ ┣ 📂srst2 ┃ ┃ ┣ 📜1160__qnrB2__qnrB2_NG_050480.1__06200__quinolone__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜1210__catA2__catA2_NG_047596.1__00164__phenicol__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜1263__aac(6')__aac(6')-IIc_NG_047273.1__04893__aminoglycoside__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜1491__arr__arr-269927220_NG_047480.1__03781__rifamycin__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜1518__ble__ble-MBL_NG_047559.1__05909__bleomycin__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜1519__qacEdelta1__qacEdelta1_NG_048042.1__05908__quaternary__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜192__ere(A)__ere(A)_NG_047763.1__03540__macrolide__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜214__ere(A)__ere(A)_NG_047764.1__03063__macrolide__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜345__blaACT__blaACT-7_NG_048630.1__00052__beta-lactam__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜356__blaACT__blaACT-56_NG_061415.1__05940__beta-lactam__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜595__blaSHV__blaSHV-39_AY150585__04999__Beta-Lactamase__ARGANNOT.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜664__sul1__sul1_NG_048082.1__04214__sulfonamide__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜688__blaSHV__blaSHV-12_NG_050590.1__00491__beta-lactam__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜767__sul2__sul2_NG_051852.1__04662__sulfonamide__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜883__aadA2__aadA2_NG_051846.1__04091__aminoglycoside__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜906__aac(3)__aac(3)-IIg_NG_047231.1__03587__aminoglycoside__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜96__mcr__mcr-9.1_MK070339.1__00225__colistin__NCBI.SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.pileup ┃ ┃ ┣ 📜SRR13183128__SRR13183128.ResGANNCBI_20210507_srst2.sorted.bam ┃ ┃ ┣ 📜SRR13183128__fullgenes__ResGANNCBI_20210507_srst2__results.txt ┃ ┃ ┗ 📜SRR13183128__genes__ResGANNCBI_20210507_srst2__results.txt ┃ ┣ 📜SRR13183128.tax ┃ ┣ 📜SRR13183128_Assembly_ratio_20210819.txt ┃ ┗ 📜SRR13183128_summaryline.csv ┣ 📂multiqc ┃ ┣ 📂multiqc_data ┃ ┃ ┣ 📜mqc_fastqc_per_base_n_content_plot_1.txt ┃ ┃ ┣ 📜mqc_fastqc_per_base_sequence_quality_plot_1.txt ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Counts.txt ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_quality_scores_plot_1.txt ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1.txt ┃ ┃ ┣ 📜mqc_fastqc_sequence_duplication_levels_plot_1.txt ┃ ┃ ┣ 📜mqc_fastqc_sequence_length_distribution_plot_1.txt ┃ ┃ ┣ 📜multiqc.log ┃ ┃ ┣ 📜multiqc_data.json ┃ ┃ ┣ 📜multiqc_fastqc.txt ┃ ┃ ┣ 📜multiqc_general_stats.txt ┃ ┃ ┗ 📜multiqc_sources.txt ┃ ┣ 📂multiqc_plots ┃ ┃ ┣ 📂pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_n_content_plot_1.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_sequence_quality_plot_1.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Counts.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Percentages.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_quality_scores_plot_1.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1_pc.pdf ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_duplication_levels_plot_1.pdf ┃ ┃ ┃ ┗ 📜mqc_fastqc_sequence_length_distribution_plot_1.pdf ┃ ┃ ┣ 📂png ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_n_content_plot_1.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_sequence_quality_plot_1.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Counts.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Percentages.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_quality_scores_plot_1.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1_pc.png ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_duplication_levels_plot_1.png ┃ ┃ ┃ ┗ 📜mqc_fastqc_sequence_length_distribution_plot_1.png ┃ ┃ ┗ 📂svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_n_content_plot_1.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_base_sequence_quality_plot_1.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Counts.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_gc_content_plot_Percentages.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_per_sequence_quality_scores_plot_1.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_counts_plot_1_pc.svg ┃ ┃ ┃ ┣ 📜mqc_fastqc_sequence_duplication_levels_plot_1.svg ┃ ┃ ┃ ┗ 📜mqc_fastqc_sequence_length_distribution_plot_1.svg ┃ ┗ 📜multiqc_report.html ┣ 📂pipeline_info ┃ ┣ 📜execution_report_2022-06-13_18-18-01.html ┃ ┣ 📜execution_report_2022-06-13_18-19-47.html ┃ ┣ 📜execution_report_2022-06-13_18-21-51.html ┃ ┣ 📜execution_report_2022-06-13_18-53-01.html ┃ ┣ 📜execution_timeline_2022-06-13_18-18-01.html ┃ ┣ 📜execution_timeline_2022-06-13_18-19-47.html ┃ ┣ 📜execution_timeline_2022-06-13_18-21-51.html ┃ ┣ 📜execution_timeline_2022-06-13_18-53-01.html ┃ ┣ 📜execution_trace_2022-06-13_18-16-05.txt ┃ ┣ 📜execution_trace_2022-06-13_18-18-01.txt ┃ ┣ 📜execution_trace_2022-06-13_18-19-47.txt ┃ ┣ 📜execution_trace_2022-06-13_18-21-51.txt ┃ ┣ 📜execution_trace_2022-06-13_18-53-01.txt ┃ ┣ 📜pipeline_dag_2022-06-13_18-18-01.svg ┃ ┣ 📜pipeline_dag_2022-06-13_18-19-47.svg ┃ ┣ 📜pipeline_dag_2022-06-13_18-21-51.svg ┃ ┣ 📜pipeline_dag_2022-06-13_18-53-01.svg ┃ ┣ 📜samplesheet.valid.csv ┃ ┗ 📜software_versions.yml ┗ 📜Phoenix_Output_Report.tsv

This is the file tree for running one sample.

Running on a High-Performance Computing (HPC) Cluster

To run PHoeNIx on an HPC and submit jobs to a cluster you will need to make config file for your executor. We provide a template in the conf folder to edit. Then run the program by running:

nextflow run CDCgov/phoenix -profile singularity,custom_HPC --input samplesheet.csv