[2024-01-25 19:24:45,020] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,022] [INFO] DQC Reference Directory: /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference
[2024-01-25 19:24:48,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,242] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,242] [INFO] Running command: gunzip -c /var/lib/cwl/stgb89548da-777d-44fa-ba2e-0a17316cbba8/GCF_014385205.1_ASM1438520v1_genomic.fna.gz | prodigal -d GCF_014385205.1_ASM1438520v1_genomic.fna/cds.fna -a GCF_014385205.1_ASM1438520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:09,413] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:09,414] [INFO] Task started: HMMsearch
[2024-01-25 19:25:09,414] [INFO] Running command: hmmsearch --tblout GCF_014385205.1_ASM1438520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/reference_markers.hmm GCF_014385205.1_ASM1438520v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:09,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:09,688] [INFO] Found 6/6 markers.
[2024-01-25 19:25:09,730] [INFO] Query marker FASTA was written to GCF_014385205.1_ASM1438520v1_genomic.fna/markers.fasta
[2024-01-25 19:25:09,731] [INFO] Task started: Blastn
[2024-01-25 19:25:09,731] [INFO] Running command: blastn -query GCF_014385205.1_ASM1438520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/reference_markers.fasta -out GCF_014385205.1_ASM1438520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:10,305] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:10,308] [INFO] Selected 10 target genomes.
[2024-01-25 19:25:10,308] [INFO] Target genome list was writen to GCF_014385205.1_ASM1438520v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:10,311] [INFO] Task started: fastANI
[2024-01-25 19:25:10,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89548da-777d-44fa-ba2e-0a17316cbba8/GCF_014385205.1_ASM1438520v1_genomic.fna.gz --refList GCF_014385205.1_ASM1438520v1_genomic.fna/target_genomes.txt --output GCF_014385205.1_ASM1438520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:21,724] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:21,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:21,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:21,732] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:21,732] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:21,732] [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
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	100.0	1627	1634	95	conclusive
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	100.0	1627	1634	95	conclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	82.6054	960	1634	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	82.5654	952	1634	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	82.4699	901	1634	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.7048	126	1634	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	79.2042	538	1634	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	76.9241	106	1634	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	76.8838	104	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:21,735] [INFO] DFAST Taxonomy check result was written to GCF_014385205.1_ASM1438520v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:21,736] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:21,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:21,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/checkm_data
[2024-01-25 19:25:21,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:21,790] [INFO] Task started: CheckM
[2024-01-25 19:25:21,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385205.1_ASM1438520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385205.1_ASM1438520v1_genomic.fna/checkm_input GCF_014385205.1_ASM1438520v1_genomic.fna/checkm_result
[2024-01-25 19:26:19,145] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:19,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:19,161] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:19,162] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:19,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385205.1_ASM1438520v1_genomic.fna/markers.fasta)
[2024-01-25 19:26:19,162] [INFO] Task started: Blastn
[2024-01-25 19:26:19,163] [INFO] Running command: blastn -query GCF_014385205.1_ASM1438520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2fc48f1-84e1-4e38-8f56-7b5980189c7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385205.1_ASM1438520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:20,017] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:20,019] [INFO] Selected 12 target genomes.
[2024-01-25 19:26:20,019] [INFO] Target genome list was writen to GCF_014385205.1_ASM1438520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:20,072] [INFO] Task started: fastANI
[2024-01-25 19:26:20,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgb89548da-777d-44fa-ba2e-0a17316cbba8/GCF_014385205.1_ASM1438520v1_genomic.fna.gz --refList GCF_014385205.1_ASM1438520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385205.1_ASM1438520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:31,708] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:31,714] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:31,715] [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_003363715.1	s__Parabacteroides acidifaciens	100.0	1627	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	conclusive
GCA_900552465.1	s__Parabacteroides sp900552465	91.0758	1075	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
GCF_014287585.1	s__Parabacteroides sp014287585	83.3492	1086	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_900760525.1	s__Parabacteroides sp900760525	82.8678	895	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCF_000154105.1	s__Parabacteroides merdae	82.6468	874	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_000156495.1	s__Parabacteroides johnsonii	82.5368	957	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_900155425.1	s__Parabacteroides massiliensis	82.3234	850	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCF_015550595.1	s__Parabacteroides sp900540715	79.2065	550	1634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:31,717] [INFO] GTDB search result was written to GCF_014385205.1_ASM1438520v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:31,721] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:31,724] [INFO] DFAST_QC result json was written to GCF_014385205.1_ASM1438520v1_genomic.fna/dqc_result.json
[2024-01-25 19:26:31,724] [INFO] DFAST_QC completed!
[2024-01-25 19:26:31,725] [INFO] Total running time: 0h1m47s