[2023-06-12 22:44:00,792] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:44:00,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:44:00,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference
[2023-06-12 22:44:03,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:44:03,140] [INFO] Task started: Prodigal
[2023-06-12 22:44:03,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b2060a9-f709-4208-950c-f154131f632e/GCA_022720235.1_ASM2272023v1_genomic.fna.gz | prodigal -d GCA_022720235.1_ASM2272023v1_genomic.fna/cds.fna -a GCA_022720235.1_ASM2272023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:44:20,772] [INFO] Task succeeded: Prodigal
[2023-06-12 22:44:20,773] [INFO] Task started: HMMsearch
[2023-06-12 22:44:20,773] [INFO] Running command: hmmsearch --tblout GCA_022720235.1_ASM2272023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/reference_markers.hmm GCA_022720235.1_ASM2272023v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:44:21,046] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:44:21,048] [INFO] Found 6/6 markers.
[2023-06-12 22:44:21,086] [INFO] Query marker FASTA was written to GCA_022720235.1_ASM2272023v1_genomic.fna/markers.fasta
[2023-06-12 22:44:21,086] [INFO] Task started: Blastn
[2023-06-12 22:44:21,087] [INFO] Running command: blastn -query GCA_022720235.1_ASM2272023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/reference_markers.fasta -out GCA_022720235.1_ASM2272023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:44:21,685] [INFO] Task succeeded: Blastn
[2023-06-12 22:44:21,690] [INFO] Selected 21 target genomes.
[2023-06-12 22:44:21,691] [INFO] Target genome list was writen to GCA_022720235.1_ASM2272023v1_genomic.fna/target_genomes.txt
[2023-06-12 22:44:21,701] [INFO] Task started: fastANI
[2023-06-12 22:44:21,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b2060a9-f709-4208-950c-f154131f632e/GCA_022720235.1_ASM2272023v1_genomic.fna.gz --refList GCA_022720235.1_ASM2272023v1_genomic.fna/target_genomes.txt --output GCA_022720235.1_ASM2272023v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:44:34,481] [INFO] Task succeeded: fastANI
[2023-06-12 22:44:34,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:44:34,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:44:34,494] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2023-06-12 22:44:34,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-12 22:44:34,495] [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 merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	98.4671	414	496	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	98.4067	416	496	95	conclusive
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	98.4012	417	496	95	conclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	90.2813	395	496	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	90.1662	393	496	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:44:34,497] [INFO] DFAST Taxonomy check result was written to GCA_022720235.1_ASM2272023v1_genomic.fna/tc_result.tsv
[2023-06-12 22:44:34,498] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:44:34,498] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:44:34,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/checkm_data
[2023-06-12 22:44:34,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:44:34,542] [INFO] Task started: CheckM
[2023-06-12 22:44:34,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720235.1_ASM2272023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720235.1_ASM2272023v1_genomic.fna/checkm_input GCA_022720235.1_ASM2272023v1_genomic.fna/checkm_result
[2023-06-12 22:45:26,726] [INFO] Task succeeded: CheckM
[2023-06-12 22:45:26,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.52%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:45:26,752] [INFO] ===== Completeness check finished =====
[2023-06-12 22:45:26,752] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:45:26,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720235.1_ASM2272023v1_genomic.fna/markers.fasta)
[2023-06-12 22:45:26,753] [INFO] Task started: Blastn
[2023-06-12 22:45:26,753] [INFO] Running command: blastn -query GCA_022720235.1_ASM2272023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd082f35c-90c7-4662-ac97-72b3e0634c8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720235.1_ASM2272023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:45:27,611] [INFO] Task succeeded: Blastn
[2023-06-12 22:45:27,616] [INFO] Selected 23 target genomes.
[2023-06-12 22:45:27,616] [INFO] Target genome list was writen to GCA_022720235.1_ASM2272023v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:45:27,658] [INFO] Task started: fastANI
[2023-06-12 22:45:27,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b2060a9-f709-4208-950c-f154131f632e/GCA_022720235.1_ASM2272023v1_genomic.fna.gz --refList GCA_022720235.1_ASM2272023v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720235.1_ASM2272023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:45:41,569] [INFO] Task succeeded: fastANI
[2023-06-12 22:45:41,579] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 22:45:41,579] [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_000154105.1	s__Parabacteroides merdae	98.4067	416	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	conclusive
GCF_000156495.1	s__Parabacteroides johnsonii	90.1662	393	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_014287585.1	s__Parabacteroides sp014287585	89.1881	389	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCF_900155425.1	s__Parabacteroides massiliensis	87.9795	382	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCA_900760525.1	s__Parabacteroides sp900760525	86.7095	359	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_910577325.1	s__Parabacteroides sp910577325	86.0509	336	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	83.5848	305	496	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 22:45:41,581] [INFO] GTDB search result was written to GCA_022720235.1_ASM2272023v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:45:41,582] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:45:41,585] [INFO] DFAST_QC result json was written to GCA_022720235.1_ASM2272023v1_genomic.fna/dqc_result.json
[2023-06-12 22:45:41,585] [INFO] DFAST_QC completed!
[2023-06-12 22:45:41,585] [INFO] Total running time: 0h1m41s