[2024-01-24 11:58:57,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference
[2024-01-24 11:58:58,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,768] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dd117b3-b901-4b75-bddf-1e5d3479d1a1/GCF_014837035.1_ASM1483703v1_genomic.fna.gz | prodigal -d GCF_014837035.1_ASM1483703v1_genomic.fna/cds.fna -a GCF_014837035.1_ASM1483703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:10,851] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:10,851] [INFO] Task started: HMMsearch
[2024-01-24 11:59:10,851] [INFO] Running command: hmmsearch --tblout GCF_014837035.1_ASM1483703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/reference_markers.hmm GCF_014837035.1_ASM1483703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:11,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:11,132] [INFO] Found 6/6 markers.
[2024-01-24 11:59:11,157] [INFO] Query marker FASTA was written to GCF_014837035.1_ASM1483703v1_genomic.fna/markers.fasta
[2024-01-24 11:59:11,158] [INFO] Task started: Blastn
[2024-01-24 11:59:11,158] [INFO] Running command: blastn -query GCF_014837035.1_ASM1483703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/reference_markers.fasta -out GCF_014837035.1_ASM1483703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:11,797] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:11,801] [INFO] Selected 20 target genomes.
[2024-01-24 11:59:11,802] [INFO] Target genome list was writen to GCF_014837035.1_ASM1483703v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:11,811] [INFO] Task started: fastANI
[2024-01-24 11:59:11,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd117b3-b901-4b75-bddf-1e5d3479d1a1/GCF_014837035.1_ASM1483703v1_genomic.fna.gz --refList GCF_014837035.1_ASM1483703v1_genomic.fna/target_genomes.txt --output GCF_014837035.1_ASM1483703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:23,601] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:23,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:23,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:23,617] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:23,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:23,617] [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 faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	78.7175	303	840	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	78.6924	306	840	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	78.0353	218	840	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	77.783	215	840	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	77.7396	200	840	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	77.5681	211	840	95	below_threshold
Chryseobacterium camelliae	strain=Dolsongi-HT1	GCA_002770595.1	1265445	1265445	type	True	77.5299	105	840	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	77.459	94	840	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	77.377	115	840	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	77.3706	179	840	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	77.3413	111	840	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	77.3003	96	840	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	77.2773	114	840	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	77.2545	180	840	95	below_threshold
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	77.2129	93	840	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	77.114	118	840	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	77.1125	116	840	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	77.1033	173	840	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	77.077	181	840	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	76.9815	114	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:23,619] [INFO] DFAST Taxonomy check result was written to GCF_014837035.1_ASM1483703v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:23,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:23,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:23,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/checkm_data
[2024-01-24 11:59:23,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:23,656] [INFO] Task started: CheckM
[2024-01-24 11:59:23,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837035.1_ASM1483703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837035.1_ASM1483703v1_genomic.fna/checkm_input GCF_014837035.1_ASM1483703v1_genomic.fna/checkm_result
[2024-01-24 12:00:01,099] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:01,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:01,118] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:01,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:01,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837035.1_ASM1483703v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:01,119] [INFO] Task started: Blastn
[2024-01-24 12:00:01,119] [INFO] Running command: blastn -query GCF_014837035.1_ASM1483703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg891584c7-b620-4eec-ad36-d66ba543e2e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837035.1_ASM1483703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:01,999] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:02,003] [INFO] Selected 17 target genomes.
[2024-01-24 12:00:02,003] [INFO] Target genome list was writen to GCF_014837035.1_ASM1483703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:02,015] [INFO] Task started: fastANI
[2024-01-24 12:00:02,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd117b3-b901-4b75-bddf-1e5d3479d1a1/GCF_014837035.1_ASM1483703v1_genomic.fna.gz --refList GCF_014837035.1_ASM1483703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837035.1_ASM1483703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:10,727] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:10,742] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:10,742] [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
GCA_014837035.1	s__Kaistella sp014837035	100.0	839	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000023725.1	s__Kaistella sp000023725	79.4964	416	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003692615.1	s__Kaistella sp003692615	79.3646	289	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019195395.1	s__Kaistella sp019195395	78.705	305	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205795.1	s__Kaistella sp002205795	78.674	307	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCA_015999765.1	s__Kaistella sp015999765	78.6204	277	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCA_002453895.1	s__Kaistella sp002453895	78.5533	306	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001403755.1	s__Kaistella senegalense	78.1484	214	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902795.1	s__Kaistella sp018902795	78.0273	294	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014695.1	s__Kaistella sp008014695	77.8753	200	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422265.1	s__Kaistella palustris	77.5433	212	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426785.1	s__Kaistella sp002426785	77.4904	160	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCA_002477665.1	s__Kaistella sp002477665	77.3061	125	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.45	96.80	0.91	0.88	5	-
GCF_003290185.1	s__Chryseobacterium lathyri	77.2705	97	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001424585.1	s__Chryseobacterium sp001424585	77.2236	140	840	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	77.2155	133	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900156725.1	s__Kaistella chaponensis	77.0913	179	840	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:10,744] [INFO] GTDB search result was written to GCF_014837035.1_ASM1483703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:10,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:10,749] [INFO] DFAST_QC result json was written to GCF_014837035.1_ASM1483703v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:10,749] [INFO] DFAST_QC completed!
[2024-01-24 12:00:10,749] [INFO] Total running time: 0h1m13s