[2023-06-05 19:01:43,300] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:43,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:43,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference
[2023-06-05 19:01:44,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:44,423] [INFO] Task started: Prodigal
[2023-06-05 19:01:44,423] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2d0bbee-67c3-4e87-b13f-99b8961dd12c/GCA_934527415.1_ERR7738140_bin.20_genomic.fna.gz | prodigal -d GCA_934527415.1_ERR7738140_bin.20_genomic.fna/cds.fna -a GCA_934527415.1_ERR7738140_bin.20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:01:49,014] [INFO] Task succeeded: Prodigal
[2023-06-05 19:01:49,015] [INFO] Task started: HMMsearch
[2023-06-05 19:01:49,015] [INFO] Running command: hmmsearch --tblout GCA_934527415.1_ERR7738140_bin.20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/reference_markers.hmm GCA_934527415.1_ERR7738140_bin.20_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:49,170] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:49,171] [INFO] Found 6/6 markers.
[2023-06-05 19:01:49,195] [INFO] Query marker FASTA was written to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/markers.fasta
[2023-06-05 19:01:49,196] [INFO] Task started: Blastn
[2023-06-05 19:01:49,196] [INFO] Running command: blastn -query GCA_934527415.1_ERR7738140_bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/reference_markers.fasta -out GCA_934527415.1_ERR7738140_bin.20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:49,718] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:49,723] [INFO] Selected 18 target genomes.
[2023-06-05 19:01:49,724] [INFO] Target genome list was writen to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/target_genomes.txt
[2023-06-05 19:01:49,734] [INFO] Task started: fastANI
[2023-06-05 19:01:49,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2d0bbee-67c3-4e87-b13f-99b8961dd12c/GCA_934527415.1_ERR7738140_bin.20_genomic.fna.gz --refList GCA_934527415.1_ERR7738140_bin.20_genomic.fna/target_genomes.txt --output GCA_934527415.1_ERR7738140_bin.20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:02:02,122] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:02,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:02:02,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:02:02,127] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 19:02:02,127] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 19:02:02,127] [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
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	98.7684	260	271	95	conclusive
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	78.1253	50	271	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	77.813	51	271	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:02:02,129] [INFO] DFAST Taxonomy check result was written to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/tc_result.tsv
[2023-06-05 19:02:02,129] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:02:02,130] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:02:02,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/checkm_data
[2023-06-05 19:02:02,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:02:02,156] [INFO] Task started: CheckM
[2023-06-05 19:02:02,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934527415.1_ERR7738140_bin.20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934527415.1_ERR7738140_bin.20_genomic.fna/checkm_input GCA_934527415.1_ERR7738140_bin.20_genomic.fna/checkm_result
[2023-06-05 19:02:20,483] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:20,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:20,503] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:20,503] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:20,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934527415.1_ERR7738140_bin.20_genomic.fna/markers.fasta)
[2023-06-05 19:02:20,504] [INFO] Task started: Blastn
[2023-06-05 19:02:20,504] [INFO] Running command: blastn -query GCA_934527415.1_ERR7738140_bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg49bea70b-e7f2-479b-b42a-2864b711fc60/dqc_reference/reference_markers_gtdb.fasta -out GCA_934527415.1_ERR7738140_bin.20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:21,245] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:21,248] [INFO] Selected 6 target genomes.
[2023-06-05 19:02:21,248] [INFO] Target genome list was writen to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:21,249] [INFO] Task started: fastANI
[2023-06-05 19:02:21,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2d0bbee-67c3-4e87-b13f-99b8961dd12c/GCA_934527415.1_ERR7738140_bin.20_genomic.fna.gz --refList GCA_934527415.1_ERR7738140_bin.20_genomic.fna/target_genomes_gtdb.txt --output GCA_934527415.1_ERR7738140_bin.20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:02:24,215] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:24,219] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:02:24,220] [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
GCF_000701705.1	s__Bilophila wadsworthia	98.7684	260	271	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	conclusive
GCA_900550745.1	s__Bilophila sp900550745	91.3585	170	271	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	97.48	97.27	0.74	0.71	3	-
GCA_900553145.1	s__Bilophila sp900553145	90.1165	218	271	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373525.1	s__Bilophila sp902373525	84.6711	204	271	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.79	98.79	0.94	0.94	2	-
GCA_019114025.1	s__Bilophila faecipullorum	82.1215	142	271	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	99.16	98.64	0.81	0.70	3	-
--------------------------------------------------------------------------------
[2023-06-05 19:02:24,221] [INFO] GTDB search result was written to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/result_gtdb.tsv
[2023-06-05 19:02:24,222] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:02:24,224] [INFO] DFAST_QC result json was written to GCA_934527415.1_ERR7738140_bin.20_genomic.fna/dqc_result.json
[2023-06-05 19:02:24,224] [INFO] DFAST_QC completed!
[2023-06-05 19:02:24,224] [INFO] Total running time: 0h0m41s