[2024-01-24 15:26:55,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,105] [INFO] DQC Reference Directory: /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference
[2024-01-24 15:26:56,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,452] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,452] [INFO] Running command: gunzip -c /var/lib/cwl/stge072533f-9f2b-498e-940a-06d75169ccf5/GCF_004349355.1_ASM434935v1_genomic.fna.gz | prodigal -d GCF_004349355.1_ASM434935v1_genomic.fna/cds.fna -a GCF_004349355.1_ASM434935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:13,236] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:13,236] [INFO] Task started: HMMsearch
[2024-01-24 15:27:13,237] [INFO] Running command: hmmsearch --tblout GCF_004349355.1_ASM434935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/reference_markers.hmm GCF_004349355.1_ASM434935v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:13,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:13,501] [INFO] Found 6/6 markers.
[2024-01-24 15:27:13,542] [INFO] Query marker FASTA was written to GCF_004349355.1_ASM434935v1_genomic.fna/markers.fasta
[2024-01-24 15:27:13,542] [INFO] Task started: Blastn
[2024-01-24 15:27:13,542] [INFO] Running command: blastn -query GCF_004349355.1_ASM434935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/reference_markers.fasta -out GCF_004349355.1_ASM434935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:14,278] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:14,282] [INFO] Selected 20 target genomes.
[2024-01-24 15:27:14,282] [INFO] Target genome list was writen to GCF_004349355.1_ASM434935v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:14,290] [INFO] Task started: fastANI
[2024-01-24 15:27:14,290] [INFO] Running command: fastANI --query /var/lib/cwl/stge072533f-9f2b-498e-940a-06d75169ccf5/GCF_004349355.1_ASM434935v1_genomic.fna.gz --refList GCF_004349355.1_ASM434935v1_genomic.fna/target_genomes.txt --output GCF_004349355.1_ASM434935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:31,198] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:31,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:31,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:31,215] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:31,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:31,215] [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 cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	100.0	1534	1536	95	conclusive
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	80.2797	650	1536	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	79.8689	640	1536	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	79.4468	627	1536	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	79.2355	522	1536	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.1655	439	1536	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.1616	515	1536	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.0221	452	1536	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	78.9027	422	1536	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	78.9002	439	1536	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.6592	415	1536	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.6427	433	1536	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	78.5529	410	1536	95	below_threshold
Flavobacterium bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	78.5362	413	1536	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	78.3777	420	1536	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	78.2566	349	1536	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.0027	350	1536	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.893	378	1536	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.7667	359	1536	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.299	179	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:31,217] [INFO] DFAST Taxonomy check result was written to GCF_004349355.1_ASM434935v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:31,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:31,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:31,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/checkm_data
[2024-01-24 15:27:31,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:31,264] [INFO] Task started: CheckM
[2024-01-24 15:27:31,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349355.1_ASM434935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349355.1_ASM434935v1_genomic.fna/checkm_input GCF_004349355.1_ASM434935v1_genomic.fna/checkm_result
[2024-01-24 15:28:20,590] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:20,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:20,611] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:20,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:20,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349355.1_ASM434935v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:20,612] [INFO] Task started: Blastn
[2024-01-24 15:28:20,612] [INFO] Running command: blastn -query GCF_004349355.1_ASM434935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd36d78a0-2974-4413-9b88-806713d7db40/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349355.1_ASM434935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:21,560] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:21,563] [INFO] Selected 16 target genomes.
[2024-01-24 15:28:21,564] [INFO] Target genome list was writen to GCF_004349355.1_ASM434935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:21,575] [INFO] Task started: fastANI
[2024-01-24 15:28:21,575] [INFO] Running command: fastANI --query /var/lib/cwl/stge072533f-9f2b-498e-940a-06d75169ccf5/GCF_004349355.1_ASM434935v1_genomic.fna.gz --refList GCF_004349355.1_ASM434935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349355.1_ASM434935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:33,966] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:33,979] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:33,979] [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_004349355.1	s__Flavobacterium cellulosilyticum	100.0	1534	1536	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_007097365.1	s__Flavobacterium franklandianum	80.2711	650	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	80.1935	582	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413745.1	s__Flavobacterium sp002413745	80.1645	617	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCF_015277675.1	s__Flavobacterium soyangense	79.9615	560	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837155.1	s__Flavobacterium sp012837155	79.5733	451	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	79.5341	508	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	79.4309	463	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	79.4156	631	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	79.1983	380	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	79.0847	446	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	78.9074	421	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	78.8857	441	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_015752255.1	s__Flavobacterium sp015752255	78.8374	427	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594725.1	s__Flavobacterium sp015594725	78.4352	355	1536	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	78.2695	351	1536	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 15:28:33,981] [INFO] GTDB search result was written to GCF_004349355.1_ASM434935v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:33,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:33,985] [INFO] DFAST_QC result json was written to GCF_004349355.1_ASM434935v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:33,986] [INFO] DFAST_QC completed!
[2024-01-24 15:28:33,986] [INFO] Total running time: 0h1m39s