[2024-01-24 13:57:56,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference
[2024-01-24 13:57:57,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,704] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg28c7e7a1-29a6-4f45-b296-f82a9a6d42cf/GCF_004745595.1_ASM474559v1_genomic.fna.gz | prodigal -d GCF_004745595.1_ASM474559v1_genomic.fna/cds.fna -a GCF_004745595.1_ASM474559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:16,430] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:16,431] [INFO] Task started: HMMsearch
[2024-01-24 13:58:16,431] [INFO] Running command: hmmsearch --tblout GCF_004745595.1_ASM474559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/reference_markers.hmm GCF_004745595.1_ASM474559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:16,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:16,708] [INFO] Found 6/6 markers.
[2024-01-24 13:58:16,743] [INFO] Query marker FASTA was written to GCF_004745595.1_ASM474559v1_genomic.fna/markers.fasta
[2024-01-24 13:58:16,744] [INFO] Task started: Blastn
[2024-01-24 13:58:16,744] [INFO] Running command: blastn -query GCF_004745595.1_ASM474559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/reference_markers.fasta -out GCF_004745595.1_ASM474559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:17,469] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:17,473] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:17,473] [INFO] Target genome list was writen to GCF_004745595.1_ASM474559v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:17,483] [INFO] Task started: fastANI
[2024-01-24 13:58:17,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c7e7a1-29a6-4f45-b296-f82a9a6d42cf/GCF_004745595.1_ASM474559v1_genomic.fna.gz --refList GCF_004745595.1_ASM474559v1_genomic.fna/target_genomes.txt --output GCF_004745595.1_ASM474559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:30,475] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:30,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:30,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:30,495] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:30,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:30,495] [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
Flavobacterium humi	strain=DS2-A	GCA_004745595.1	2562683	2562683	type	True	100.0	1179	1181	95	conclusive
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	78.3994	232	1181	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	78.0991	205	1181	95	below_threshold
Flavobacterium psychrophilum	strain=FPG3	GCA_000754405.1	96345	96345	type	True	78.0836	212	1181	95	below_threshold
Flavobacterium psychrophilum	strain=ATCC 49418	GCA_002217405.1	96345	96345	type	True	78.0434	204	1181	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.9624	283	1181	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	77.7842	245	1181	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	77.7758	245	1181	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	77.7722	243	1181	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	77.7668	153	1181	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	77.6727	248	1181	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.6088	118	1181	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.5249	182	1181	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	77.4607	184	1181	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	77.4306	223	1181	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.4234	118	1181	95	below_threshold
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	77.3608	232	1181	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	77.3443	182	1181	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	77.298	222	1181	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	77.0859	156	1181	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.032	155	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:30,497] [INFO] DFAST Taxonomy check result was written to GCF_004745595.1_ASM474559v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:30,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:30,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:30,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/checkm_data
[2024-01-24 13:58:30,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:30,544] [INFO] Task started: CheckM
[2024-01-24 13:58:30,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004745595.1_ASM474559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004745595.1_ASM474559v1_genomic.fna/checkm_input GCF_004745595.1_ASM474559v1_genomic.fna/checkm_result
[2024-01-24 13:59:21,660] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:21,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:21,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:21,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004745595.1_ASM474559v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:21,687] [INFO] Task started: Blastn
[2024-01-24 13:59:21,687] [INFO] Running command: blastn -query GCF_004745595.1_ASM474559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f83369-6ef1-4f82-b415-a76bcc9a48c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004745595.1_ASM474559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:22,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:22,716] [INFO] Selected 21 target genomes.
[2024-01-24 13:59:22,716] [INFO] Target genome list was writen to GCF_004745595.1_ASM474559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:22,778] [INFO] Task started: fastANI
[2024-01-24 13:59:22,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c7e7a1-29a6-4f45-b296-f82a9a6d42cf/GCF_004745595.1_ASM474559v1_genomic.fna.gz --refList GCF_004745595.1_ASM474559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004745595.1_ASM474559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:35,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:35,155] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:35,156] [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_004745595.1	s__Flavobacterium humi	100.0	1179	1181	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_004122165.1	s__Flavobacterium sp004122165	78.3989	231	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	78.0971	204	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217405.1	s__Flavobacterium psychrophilum	78.032	204	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.22	98.91	0.92	0.83	157	-
GCF_017875765.1	s__Flavobacterium sp017875765	77.8814	147	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_900100625.1	s__Flavobacterium saliperosum	77.7984	244	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011392115.1	s__Flavobacterium sp011392115	77.7545	100	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959765.1	s__Flavobacterium sp004959765	77.7527	202	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303755.1	s__Flavobacterium sp017303755	77.7081	130	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833415.1	s__Flavobacterium sp017833415	77.7033	164	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013389455.1	s__Flavobacterium sp001898245	77.6975	219	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	-
GCF_000498475.1	s__Flavobacterium cauense	77.6828	246	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCA_018062725.1	s__Flavobacterium sp018062725	77.5718	162	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.43	180	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498495.1	s__Flavobacterium enshiense	77.4255	222	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000498535.1	s__Flavobacterium limnosediminis	77.3558	231	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787805.1	s__Flavobacterium sp016787805	77.3505	142	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	77.0216	154	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_903902795.1	s__Flavobacterium sp903902795	76.8555	111	1181	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	76.6541	88	1181	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	76.4765	150	1181	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 13:59:35,158] [INFO] GTDB search result was written to GCF_004745595.1_ASM474559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:35,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:35,163] [INFO] DFAST_QC result json was written to GCF_004745595.1_ASM474559v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:35,164] [INFO] DFAST_QC completed!
[2024-01-24 13:59:35,164] [INFO] Total running time: 0h1m39s