[2024-01-24 12:06:35,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:35,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:35,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference
[2024-01-24 12:06:36,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,544] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg71034a6f-9d5b-4ab5-bec7-2c105ac9a6fd/GCF_003336205.1_ASM333620v1_genomic.fna.gz | prodigal -d GCF_003336205.1_ASM333620v1_genomic.fna/cds.fna -a GCF_003336205.1_ASM333620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:47,206] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:47,207] [INFO] Task started: HMMsearch
[2024-01-24 12:06:47,207] [INFO] Running command: hmmsearch --tblout GCF_003336205.1_ASM333620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/reference_markers.hmm GCF_003336205.1_ASM333620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:47,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:47,443] [INFO] Found 6/6 markers.
[2024-01-24 12:06:47,469] [INFO] Query marker FASTA was written to GCF_003336205.1_ASM333620v1_genomic.fna/markers.fasta
[2024-01-24 12:06:47,469] [INFO] Task started: Blastn
[2024-01-24 12:06:47,469] [INFO] Running command: blastn -query GCF_003336205.1_ASM333620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/reference_markers.fasta -out GCF_003336205.1_ASM333620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:48,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:48,129] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:48,130] [INFO] Target genome list was writen to GCF_003336205.1_ASM333620v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:48,138] [INFO] Task started: fastANI
[2024-01-24 12:06:48,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg71034a6f-9d5b-4ab5-bec7-2c105ac9a6fd/GCF_003336205.1_ASM333620v1_genomic.fna.gz --refList GCF_003336205.1_ASM333620v1_genomic.fna/target_genomes.txt --output GCF_003336205.1_ASM333620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:58,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:58,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:58,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:58,372] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:58,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:58,373] [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
Chryseobacterium lacus	strain=YLOS41	GCA_003984675.1	2058346	2058346	type	True	100.0	778	778	95	conclusive
Chryseobacterium lacus	strain=YLOS41	GCA_003336205.1	2058346	2058346	type	True	100.0	778	778	95	conclusive
Chryseobacterium taklimakanense	strain=NCTC13490	GCA_900187185.1	536441	536441	type	True	78.6389	185	778	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.5652	149	778	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.5586	148	778	95	below_threshold
Chryseobacterium echinoideorum	strain=CC-CZW010	GCA_007474535.1	1549648	1549648	type	True	77.5013	138	778	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	77.0947	139	778	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.091	126	778	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	77.0689	141	778	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	77.0379	112	778	95	below_threshold
Chryseobacterium indologenes	strain=NCTC10796	GCA_900460995.1	253	253	type	True	76.9943	114	778	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	76.9895	124	778	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	76.9429	133	778	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	76.8856	138	778	95	below_threshold
Chryseobacterium daecheongense	strain=DSM 15235	GCA_003729955.1	192389	192389	type	True	76.8652	121	778	95	below_threshold
Chryseobacterium daecheongense	strain=DSM 15235	GCA_004365465.1	192389	192389	type	True	76.8632	122	778	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	76.8416	154	778	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	76.6946	125	778	95	below_threshold
Chryseobacterium gregarium	strain=DSM 19109	GCA_000430845.1	456299	456299	type	True	76.6636	126	778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:58,375] [INFO] DFAST Taxonomy check result was written to GCF_003336205.1_ASM333620v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:58,376] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:58,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:58,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/checkm_data
[2024-01-24 12:06:58,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:58,406] [INFO] Task started: CheckM
[2024-01-24 12:06:58,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336205.1_ASM333620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336205.1_ASM333620v1_genomic.fna/checkm_input GCF_003336205.1_ASM333620v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,938] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,958] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336205.1_ASM333620v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,959] [INFO] Task started: Blastn
[2024-01-24 12:07:33,959] [INFO] Running command: blastn -query GCF_003336205.1_ASM333620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb247b768-2ea4-42ac-bfa0-f761c1ce1e4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336205.1_ASM333620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,812] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:34,812] [INFO] Target genome list was writen to GCF_003336205.1_ASM333620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,825] [INFO] Task started: fastANI
[2024-01-24 12:07:34,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg71034a6f-9d5b-4ab5-bec7-2c105ac9a6fd/GCF_003336205.1_ASM333620v1_genomic.fna.gz --refList GCF_003336205.1_ASM333620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336205.1_ASM333620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:44,398] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:44,413] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:44,413] [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_003336205.1	s__Planobacterium lacus	100.0	778	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Planobacterium	95.0	98.17	96.96	0.92	0.87	4	conclusive
GCA_015478785.1	s__Planobacterium sp015478785	94.5388	540	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Planobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187185.1	s__Planobacterium taklimakanense	78.7033	183	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Planobacterium	95.0	96.53	96.28	0.85	0.83	3	-
GCA_002197835.1	s__Kaistella sp002197835	77.8251	161	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCF_019195395.1	s__Kaistella sp019195395	77.5586	148	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007474535.1	s__Chryseobacterium echinoideorum	77.5009	138	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898255.1	s__Kaistella sp001898255	77.4023	116	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.97	99.97	0.99	0.99	2	-
GCA_018902795.1	s__Kaistella sp018902795	77.2671	174	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	77.1028	113	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	77.0107	123	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCA_002426785.1	s__Kaistella sp002426785	76.9053	139	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCF_001421435.1	s__Chryseobacterium sp001421435	76.8864	140	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003729955.1	s__Chryseobacterium daecheongense	76.8832	121	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116415.1	s__Chryseobacterium formosense	76.8577	153	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCA_002439165.1	s__Chryseobacterium indologenes_E	76.7291	130	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679325.1	s__Kaistella gelatinilytica	76.7046	133	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	76.6788	164	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCA_002337005.1	s__Cloacibacterium sp002337005	76.1334	83	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,415] [INFO] GTDB search result was written to GCF_003336205.1_ASM333620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:44,416] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:44,420] [INFO] DFAST_QC result json was written to GCF_003336205.1_ASM333620v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:44,420] [INFO] DFAST_QC completed!
[2024-01-24 12:07:44,420] [INFO] Total running time: 0h1m9s