[2023-06-05 18:46:11,498] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:46:11,515] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:46:11,515] [INFO] DQC Reference Directory: /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference
[2023-06-05 18:46:14,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:46:14,643] [INFO] Task started: Prodigal
[2023-06-05 18:46:14,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b51fd90-1723-4f0b-9b7b-f2c810ebbed8/GCA_934838855.1_MTG225_bin.34.fa_genomic.fna.gz | prodigal -d GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/cds.fna -a GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:46:23,923] [INFO] Task succeeded: Prodigal
[2023-06-05 18:46:23,924] [INFO] Task started: HMMsearch
[2023-06-05 18:46:23,924] [INFO] Running command: hmmsearch --tblout GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/reference_markers.hmm GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:46:24,464] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:46:24,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b51fd90-1723-4f0b-9b7b-f2c810ebbed8/GCA_934838855.1_MTG225_bin.34.fa_genomic.fna.gz]
[2023-06-05 18:46:24,509] [INFO] Query marker FASTA was written to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/markers.fasta
[2023-06-05 18:46:24,510] [INFO] Task started: Blastn
[2023-06-05 18:46:24,510] [INFO] Running command: blastn -query GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/reference_markers.fasta -out GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:46:26,226] [INFO] Task succeeded: Blastn
[2023-06-05 18:46:26,234] [INFO] Selected 28 target genomes.
[2023-06-05 18:46:26,234] [INFO] Target genome list was writen to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:46:26,245] [INFO] Task started: fastANI
[2023-06-05 18:46:26,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b51fd90-1723-4f0b-9b7b-f2c810ebbed8/GCA_934838855.1_MTG225_bin.34.fa_genomic.fna.gz --refList GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/target_genomes.txt --output GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:46:54,464] [INFO] Task succeeded: fastANI
[2023-06-05 18:46:54,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:46:54,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:46:54,468] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:46:54,468] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:46:54,469] [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
--------------------------------------------------------------------------------
[2023-06-05 18:46:54,471] [INFO] DFAST Taxonomy check result was written to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:46:54,472] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:46:54,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:46:54,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/checkm_data
[2023-06-05 18:46:54,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:46:54,504] [INFO] Task started: CheckM
[2023-06-05 18:46:54,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/checkm_input GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/checkm_result
[2023-06-05 18:47:35,729] [INFO] Task succeeded: CheckM
[2023-06-05 18:47:35,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:47:35,774] [INFO] ===== Completeness check finished =====
[2023-06-05 18:47:35,774] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:47:35,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/markers.fasta)
[2023-06-05 18:47:35,775] [INFO] Task started: Blastn
[2023-06-05 18:47:35,775] [INFO] Running command: blastn -query GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgcaf58815-2a02-47c1-b29b-38b8ab1245b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:47:36,762] [INFO] Task succeeded: Blastn
[2023-06-05 18:47:36,767] [INFO] Selected 12 target genomes.
[2023-06-05 18:47:36,767] [INFO] Target genome list was writen to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:47:36,776] [INFO] Task started: fastANI
[2023-06-05 18:47:36,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b51fd90-1723-4f0b-9b7b-f2c810ebbed8/GCA_934838855.1_MTG225_bin.34.fa_genomic.fna.gz --refList GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:47:44,154] [INFO] Task succeeded: fastANI
[2023-06-05 18:47:44,165] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:47:44,165] [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_900542445.1	s__Ventricola sp900542445	98.2447	522	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.97	98.40	0.91	0.87	4	conclusive
GCA_900542395.1	s__Ventricola sp900542395	86.6283	405	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.33	97.06	0.84	0.79	5	-
GCA_900548125.1	s__Ventricola sp900548125	83.0735	297	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.02	96.93	0.87	0.87	4	-
GCA_004555535.1	s__Ventricola sp004555535	80.1189	269	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556985.1	s__Ventricola sp004556985	79.9134	259	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937505.1	s__Ventricola sp017937505	79.7516	246	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716525.1	s__Ventricola gallistercoris	79.4467	200	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412025.1	s__Ventricola sp017412025	78.9173	219	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056305.1	s__Ventricola sp015056305	78.658	206	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521565.1	s__Ventricola sp017521565	78.6342	196	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715105.1	s__Ventricola intestinavium	78.5886	172	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938795.1	s__Ventricola sp017938795	78.5615	180	627	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:47:44,167] [INFO] GTDB search result was written to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:47:44,168] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:47:44,170] [INFO] DFAST_QC result json was written to GCA_934838855.1_MTG225_bin.34.fa_genomic.fna/dqc_result.json
[2023-06-05 18:47:44,171] [INFO] DFAST_QC completed!
[2023-06-05 18:47:44,171] [INFO] Total running time: 0h1m33s