[2023-06-28 12:04:01,969] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:04:01,971] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:04:01,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference
[2023-06-28 12:04:03,339] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:04:03,340] [INFO] Task started: Prodigal
[2023-06-28 12:04:03,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea4c175-c0e3-4df7-97ae-8d423f6f897e/GCA_017621205.1_ASM1762120v1_genomic.fna.gz | prodigal -d GCA_017621205.1_ASM1762120v1_genomic.fna/cds.fna -a GCA_017621205.1_ASM1762120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:04:11,262] [INFO] Task succeeded: Prodigal
[2023-06-28 12:04:11,262] [INFO] Task started: HMMsearch
[2023-06-28 12:04:11,263] [INFO] Running command: hmmsearch --tblout GCA_017621205.1_ASM1762120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/reference_markers.hmm GCA_017621205.1_ASM1762120v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:04:11,517] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:04:11,519] [INFO] Found 6/6 markers.
[2023-06-28 12:04:11,555] [INFO] Query marker FASTA was written to GCA_017621205.1_ASM1762120v1_genomic.fna/markers.fasta
[2023-06-28 12:04:11,555] [INFO] Task started: Blastn
[2023-06-28 12:04:11,556] [INFO] Running command: blastn -query GCA_017621205.1_ASM1762120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/reference_markers.fasta -out GCA_017621205.1_ASM1762120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:12,163] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:12,168] [INFO] Selected 27 target genomes.
[2023-06-28 12:04:12,168] [INFO] Target genome list was writen to GCA_017621205.1_ASM1762120v1_genomic.fna/target_genomes.txt
[2023-06-28 12:04:12,174] [INFO] Task started: fastANI
[2023-06-28 12:04:12,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea4c175-c0e3-4df7-97ae-8d423f6f897e/GCA_017621205.1_ASM1762120v1_genomic.fna.gz --refList GCA_017621205.1_ASM1762120v1_genomic.fna/target_genomes.txt --output GCA_017621205.1_ASM1762120v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:26,077] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:26,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:26,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:26,081] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:26,081] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:04:26,081] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-28 12:04:26,084] [INFO] DFAST Taxonomy check result was written to GCA_017621205.1_ASM1762120v1_genomic.fna/tc_result.tsv
[2023-06-28 12:04:26,085] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:26,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:26,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/checkm_data
[2023-06-28 12:04:26,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:26,127] [INFO] Task started: CheckM
[2023-06-28 12:04:26,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621205.1_ASM1762120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621205.1_ASM1762120v1_genomic.fna/checkm_input GCA_017621205.1_ASM1762120v1_genomic.fna/checkm_result
[2023-06-28 12:04:54,087] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:54,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:54,116] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:54,116] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:54,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621205.1_ASM1762120v1_genomic.fna/markers.fasta)
[2023-06-28 12:04:54,117] [INFO] Task started: Blastn
[2023-06-28 12:04:54,117] [INFO] Running command: blastn -query GCA_017621205.1_ASM1762120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e44040-643e-4229-b914-04287eb11897/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621205.1_ASM1762120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:54,904] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:54,909] [INFO] Selected 23 target genomes.
[2023-06-28 12:04:54,909] [INFO] Target genome list was writen to GCA_017621205.1_ASM1762120v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:54,927] [INFO] Task started: fastANI
[2023-06-28 12:04:54,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea4c175-c0e3-4df7-97ae-8d423f6f897e/GCA_017621205.1_ASM1762120v1_genomic.fna.gz --refList GCA_017621205.1_ASM1762120v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621205.1_ASM1762120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:05:07,263] [INFO] Task succeeded: fastANI
[2023-06-28 12:05:07,268] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:05:07,268] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_017621205.1	s__NC2004 sp017621205	100.0	1049	1049	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__NC2004	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000621905.1	s__NC2004 sp000621905	77.1846	65	1049	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__NC2004	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:05:07,284] [INFO] GTDB search result was written to GCA_017621205.1_ASM1762120v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:05:07,285] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:05:07,289] [INFO] DFAST_QC result json was written to GCA_017621205.1_ASM1762120v1_genomic.fna/dqc_result.json
[2023-06-28 12:05:07,289] [INFO] DFAST_QC completed!
[2023-06-28 12:05:07,289] [INFO] Total running time: 0h1m5s