[2024-01-24 13:10:03,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,883] [INFO] DQC Reference Directory: /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference
[2024-01-24 13:10:05,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,224] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aa43390-84db-4ad8-ab8b-388bfd075c34/GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/cds.fna -a GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:22,806] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:22,807] [INFO] Task started: HMMsearch
[2024-01-24 13:10:22,807] [INFO] Running command: hmmsearch --tblout GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/reference_markers.hmm GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:23,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:23,166] [INFO] Found 6/6 markers.
[2024-01-24 13:10:23,200] [INFO] Query marker FASTA was written to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:23,201] [INFO] Task started: Blastn
[2024-01-24 13:10:23,201] [INFO] Running command: blastn -query GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/reference_markers.fasta -out GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:23,818] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:23,822] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:23,822] [INFO] Target genome list was writen to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:23,829] [INFO] Task started: fastANI
[2024-01-24 13:10:23,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa43390-84db-4ad8-ab8b-388bfd075c34/GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna.gz --refList GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:35,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:35,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:35,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:35,169] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:35,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:35,169] [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 johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	77.8553	117	1283	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.8277	112	1283	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	77.686	117	1283	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	77.658	118	1283	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.6205	169	1283	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.4881	171	1283	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	77.4665	170	1283	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	77.4326	174	1283	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	77.4098	174	1283	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.312	168	1283	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	75.8036	50	1283	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	75.7875	50	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:35,172] [INFO] DFAST Taxonomy check result was written to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:35,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:35,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:35,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/checkm_data
[2024-01-24 13:10:35,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:35,219] [INFO] Task started: CheckM
[2024-01-24 13:10:35,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/checkm_input GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:11:26,923] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:26,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:26,945] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:26,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:26,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:11:26,946] [INFO] Task started: Blastn
[2024-01-24 13:11:26,946] [INFO] Running command: blastn -query GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga944877b-815d-47a9-a47a-aa1b30bd658c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:27,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:27,823] [INFO] Selected 23 target genomes.
[2024-01-24 13:11:27,823] [INFO] Target genome list was writen to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:27,842] [INFO] Task started: fastANI
[2024-01-24 13:11:27,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa43390-84db-4ad8-ab8b-388bfd075c34/GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna.gz --refList GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:42,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:42,025] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:42,025] [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_013409575.1	s__Macellibacteroides fermentans	97.2811	1075	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	96.90	95.56	0.80	0.74	5	conclusive
GCA_018054455.1	s__Macellibacteroides sp018054455	80.9675	496	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Macellibacteroides	95.0	98.91	97.71	0.78	0.74	5	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.8065	117	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_000154105.1	s__Parabacteroides merdae	77.6485	117	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_003473295.1	s__Parabacteroides sp003473295	77.6472	131	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647375.1	s__Parabacteroides faecis	77.6073	168	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCF_900128505.1	s__Parabacteroides timonensis	77.5148	168	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_015550595.1	s__Parabacteroides sp900540715	77.5065	173	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_000969825.1	s__Parabacteroides gordonii	77.433	174	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_000969835.1	s__Parabacteroides goldsteinii	77.3201	166	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCA_900760525.1	s__Parabacteroides sp900760525	77.2994	111	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.1011	81	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:42,027] [INFO] GTDB search result was written to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:42,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:42,031] [INFO] DFAST_QC result json was written to GCF_900168155.1_IMG-taxon_2595698220_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:42,031] [INFO] DFAST_QC completed!
[2024-01-24 13:11:42,031] [INFO] Total running time: 0h1m38s