[2024-01-24 11:22:49,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,480] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference
[2024-01-24 11:22:50,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,687] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,687] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf1362c7-a47e-4e2c-aeb8-5c42682a7380/GCF_013401995.1_ASM1340199v1_genomic.fna.gz | prodigal -d GCF_013401995.1_ASM1340199v1_genomic.fna/cds.fna -a GCF_013401995.1_ASM1340199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:13,870] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:13,870] [INFO] Task started: HMMsearch
[2024-01-24 11:23:13,871] [INFO] Running command: hmmsearch --tblout GCF_013401995.1_ASM1340199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/reference_markers.hmm GCF_013401995.1_ASM1340199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:14,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:14,129] [INFO] Found 6/6 markers.
[2024-01-24 11:23:14,164] [INFO] Query marker FASTA was written to GCF_013401995.1_ASM1340199v1_genomic.fna/markers.fasta
[2024-01-24 11:23:14,164] [INFO] Task started: Blastn
[2024-01-24 11:23:14,165] [INFO] Running command: blastn -query GCF_013401995.1_ASM1340199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/reference_markers.fasta -out GCF_013401995.1_ASM1340199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:14,790] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:14,793] [INFO] Selected 16 target genomes.
[2024-01-24 11:23:14,794] [INFO] Target genome list was writen to GCF_013401995.1_ASM1340199v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:14,799] [INFO] Task started: fastANI
[2024-01-24 11:23:14,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1362c7-a47e-4e2c-aeb8-5c42682a7380/GCF_013401995.1_ASM1340199v1_genomic.fna.gz --refList GCF_013401995.1_ASM1340199v1_genomic.fna/target_genomes.txt --output GCF_013401995.1_ASM1340199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:24,667] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:24,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:24,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:24,684] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:23:24,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:24,684] [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
Flavobacterium agri	strain=MAH-1	GCA_013401995.1	2743471	2743471	type	True	100.0	1306	1306	95	conclusive
Flavobacterium agri	strain=MAH-1	GCA_013366395.1	2743471	2743471	type	True	99.9959	1292	1306	95	conclusive
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	77.9734	324	1306	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	77.555	303	1306	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	77.0554	203	1306	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	77.0234	208	1306	95	below_threshold
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	76.898	148	1306	95	below_threshold
Flavobacterium suncheonense	strain=DSM 17707	GCA_000430025.1	350894	350894	type	True	76.857	109	1306	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	76.8483	107	1306	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	76.7113	52	1306	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	76.7104	62	1306	95	below_threshold
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	76.6176	135	1306	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	76.5012	60	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:24,686] [INFO] DFAST Taxonomy check result was written to GCF_013401995.1_ASM1340199v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:24,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:24,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:24,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/checkm_data
[2024-01-24 11:23:24,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:24,732] [INFO] Task started: CheckM
[2024-01-24 11:23:24,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013401995.1_ASM1340199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013401995.1_ASM1340199v1_genomic.fna/checkm_input GCF_013401995.1_ASM1340199v1_genomic.fna/checkm_result
[2024-01-24 11:24:28,086] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:28,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:28,107] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:28,108] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:28,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013401995.1_ASM1340199v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:28,108] [INFO] Task started: Blastn
[2024-01-24 11:24:28,109] [INFO] Running command: blastn -query GCF_013401995.1_ASM1340199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c1a91b-c936-4fb3-ab3c-25171af98903/dqc_reference/reference_markers_gtdb.fasta -out GCF_013401995.1_ASM1340199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:29,034] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:29,038] [INFO] Selected 9 target genomes.
[2024-01-24 11:24:29,039] [INFO] Target genome list was writen to GCF_013401995.1_ASM1340199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:29,082] [INFO] Task started: fastANI
[2024-01-24 11:24:29,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1362c7-a47e-4e2c-aeb8-5c42682a7380/GCF_013401995.1_ASM1340199v1_genomic.fna.gz --refList GCF_013401995.1_ASM1340199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013401995.1_ASM1340199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:36,543] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:36,554] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:36,554] [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_013401995.1	s__Flavobacterium agri	100.0	1306	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_004295795.1	s__Flavobacterium sp004295795	80.3095	773	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014748335.1	s__Flavobacterium sp014748335	79.8456	693	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211145.1	s__Flavobacterium sp004211145	79.7045	644	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911565.1	s__Flavobacterium sp012911565	77.9459	329	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101895.1	s__Flavobacterium caeni	77.5531	304	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430025.1	s__Flavobacterium suncheonense	76.857	109	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002483285.1	s__Flavobacterium sp002483285	76.7284	216	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234525.1	s__Flavobacterium sp015234525	76.6607	94	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:36,556] [INFO] GTDB search result was written to GCF_013401995.1_ASM1340199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:36,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:36,560] [INFO] DFAST_QC result json was written to GCF_013401995.1_ASM1340199v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:36,560] [INFO] DFAST_QC completed!
[2024-01-24 11:24:36,560] [INFO] Total running time: 0h1m47s