[2024-01-24 13:56:13,194] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference
[2024-01-24 13:56:14,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,467] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d9a47fe-a639-4e4b-a049-de1eaf530653/GCF_014748335.1_ASM1474833v1_genomic.fna.gz | prodigal -d GCF_014748335.1_ASM1474833v1_genomic.fna/cds.fna -a GCF_014748335.1_ASM1474833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:35,461] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:35,462] [INFO] Task started: HMMsearch
[2024-01-24 13:56:35,462] [INFO] Running command: hmmsearch --tblout GCF_014748335.1_ASM1474833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/reference_markers.hmm GCF_014748335.1_ASM1474833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:35,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:35,753] [INFO] Found 6/6 markers.
[2024-01-24 13:56:35,786] [INFO] Query marker FASTA was written to GCF_014748335.1_ASM1474833v1_genomic.fna/markers.fasta
[2024-01-24 13:56:35,786] [INFO] Task started: Blastn
[2024-01-24 13:56:35,786] [INFO] Running command: blastn -query GCF_014748335.1_ASM1474833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/reference_markers.fasta -out GCF_014748335.1_ASM1474833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:36,437] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:36,442] [INFO] Selected 23 target genomes.
[2024-01-24 13:56:36,442] [INFO] Target genome list was writen to GCF_014748335.1_ASM1474833v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:36,456] [INFO] Task started: fastANI
[2024-01-24 13:56:36,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d9a47fe-a639-4e4b-a049-de1eaf530653/GCF_014748335.1_ASM1474833v1_genomic.fna.gz --refList GCF_014748335.1_ASM1474833v1_genomic.fna/target_genomes.txt --output GCF_014748335.1_ASM1474833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:49,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:49,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:49,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:49,683] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:56:49,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:56:49,683] [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_013366395.1	2743471	2743471	type	True	79.8577	696	1238	95	below_threshold
Flavobacterium agri	strain=MAH-1	GCA_013401995.1	2743471	2743471	type	True	79.8533	701	1238	95	below_threshold
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	77.43	255	1238	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	77.2929	259	1238	95	below_threshold
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	76.8886	66	1238	95	below_threshold
Flavobacterium stagni	strain=WWJ-16	GCA_004122105.1	2506421	2506421	type	True	76.8842	58	1238	95	below_threshold
Flavobacterium pallidum	strain=HYN0049	GCA_003097535.1	2172098	2172098	type	True	76.8327	116	1238	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	76.8045	179	1238	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	76.7916	182	1238	95	below_threshold
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	76.6454	102	1238	95	below_threshold
Flavobacterium humi	strain=DS2-A	GCA_004745595.1	2562683	2562683	type	True	76.5825	90	1238	95	below_threshold
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	76.5475	121	1238	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	76.5231	92	1238	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	76.4977	84	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,685] [INFO] DFAST Taxonomy check result was written to GCF_014748335.1_ASM1474833v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:49,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:49,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:49,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/checkm_data
[2024-01-24 13:56:49,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:49,725] [INFO] Task started: CheckM
[2024-01-24 13:56:49,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014748335.1_ASM1474833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014748335.1_ASM1474833v1_genomic.fna/checkm_input GCF_014748335.1_ASM1474833v1_genomic.fna/checkm_result
[2024-01-24 13:57:48,929] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:48,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,951] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:48,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:48,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014748335.1_ASM1474833v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:48,953] [INFO] Task started: Blastn
[2024-01-24 13:57:48,953] [INFO] Running command: blastn -query GCF_014748335.1_ASM1474833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49622058-5262-42b6-962b-9e19102fef7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014748335.1_ASM1474833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:49,841] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:49,845] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:49,845] [INFO] Target genome list was writen to GCF_014748335.1_ASM1474833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:49,853] [INFO] Task started: fastANI
[2024-01-24 13:57:49,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d9a47fe-a639-4e4b-a049-de1eaf530653/GCF_014748335.1_ASM1474833v1_genomic.fna.gz --refList GCF_014748335.1_ASM1474833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014748335.1_ASM1474833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:58,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:58,019] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:58,020] [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_014748335.1	s__Flavobacterium sp014748335	100.0	1237	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013401995.1	s__Flavobacterium agri	79.8496	701	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004295795.1	s__Flavobacterium sp004295795	79.476	664	1238	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	78.4471	511	1238	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	77.4387	255	1238	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	77.3149	82	1238	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	77.2923	259	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483285.1	s__Flavobacterium sp002483285	76.9129	150	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100375.1	s__Flavobacterium noncentrifugens	76.7916	182	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003055625.1	s__Flavobacterium magnum	76.522	120	1238	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 13:57:58,021] [INFO] GTDB search result was written to GCF_014748335.1_ASM1474833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:58,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:58,025] [INFO] DFAST_QC result json was written to GCF_014748335.1_ASM1474833v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:58,025] [INFO] DFAST_QC completed!
[2024-01-24 13:57:58,025] [INFO] Total running time: 0h1m45s