[2024-01-25 19:45:50,434] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,436] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference
[2024-01-25 19:45:51,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,572] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg8202cd2d-0b7e-4c95-91aa-6991151bf786/GCF_022513635.1_ASM2251363v1_genomic.fna.gz | prodigal -d GCF_022513635.1_ASM2251363v1_genomic.fna/cds.fna -a GCF_022513635.1_ASM2251363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:07,307] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:07,307] [INFO] Task started: HMMsearch
[2024-01-25 19:46:07,307] [INFO] Running command: hmmsearch --tblout GCF_022513635.1_ASM2251363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/reference_markers.hmm GCF_022513635.1_ASM2251363v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:07,547] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:07,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8202cd2d-0b7e-4c95-91aa-6991151bf786/GCF_022513635.1_ASM2251363v1_genomic.fna.gz]
[2024-01-25 19:46:07,587] [INFO] Query marker FASTA was written to GCF_022513635.1_ASM2251363v1_genomic.fna/markers.fasta
[2024-01-25 19:46:07,587] [INFO] Task started: Blastn
[2024-01-25 19:46:07,587] [INFO] Running command: blastn -query GCF_022513635.1_ASM2251363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/reference_markers.fasta -out GCF_022513635.1_ASM2251363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:08,162] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:08,164] [INFO] Selected 23 target genomes.
[2024-01-25 19:46:08,165] [INFO] Target genome list was writen to GCF_022513635.1_ASM2251363v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:08,175] [INFO] Task started: fastANI
[2024-01-25 19:46:08,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg8202cd2d-0b7e-4c95-91aa-6991151bf786/GCF_022513635.1_ASM2251363v1_genomic.fna.gz --refList GCF_022513635.1_ASM2251363v1_genomic.fna/target_genomes.txt --output GCF_022513635.1_ASM2251363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:29,818] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:29,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:29,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:29,829] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:29,829] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:29,829] [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
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	100.0	1508	1509	95	conclusive
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	77.9439	375	1509	95	below_threshold
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	77.6481	398	1509	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	77.1878	96	1509	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.6317	71	1509	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.5569	86	1509	95	below_threshold
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	76.3337	50	1509	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.2139	90	1509	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.2116	104	1509	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	76.1119	73	1509	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.041	64	1509	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.9001	52	1509	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	75.7805	50	1509	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.5827	59	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:29,831] [INFO] DFAST Taxonomy check result was written to GCF_022513635.1_ASM2251363v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:29,831] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:29,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:29,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/checkm_data
[2024-01-25 19:46:29,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:29,874] [INFO] Task started: CheckM
[2024-01-25 19:46:29,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022513635.1_ASM2251363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022513635.1_ASM2251363v1_genomic.fna/checkm_input GCF_022513635.1_ASM2251363v1_genomic.fna/checkm_result
[2024-01-25 19:47:15,754] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:15,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:15,772] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:15,772] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:15,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022513635.1_ASM2251363v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:15,773] [INFO] Task started: Blastn
[2024-01-25 19:47:15,773] [INFO] Running command: blastn -query GCF_022513635.1_ASM2251363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ecf570a-bb1f-4149-9dc0-0c41bef4cf01/dqc_reference/reference_markers_gtdb.fasta -out GCF_022513635.1_ASM2251363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:16,714] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:16,716] [INFO] Selected 31 target genomes.
[2024-01-25 19:47:16,716] [INFO] Target genome list was writen to GCF_022513635.1_ASM2251363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:16,751] [INFO] Task started: fastANI
[2024-01-25 19:47:16,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg8202cd2d-0b7e-4c95-91aa-6991151bf786/GCF_022513635.1_ASM2251363v1_genomic.fna.gz --refList GCF_022513635.1_ASM2251363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022513635.1_ASM2251363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:38,569] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:38,582] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:47:38,583] [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_003349965.1	s__Niabella yanshanensis	77.6559	397	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	77.3159	96	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719165.1	s__JJ008 sp016719165	76.9086	50	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_002400415.1	s__JJ008 sp002400415	76.864	59	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	76.701	59	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826165.1	s__JJ008 sp902826165	76.6887	56	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896965.1	s__Niabella sp001896965	76.5591	90	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713085.1	s__Lacibacter sp016713085	76.5489	66	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075435.1	s__Agriterribacter sp003075435	76.4974	65	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	97.00	96.97	0.82	0.82	3	-
GCA_002399735.1	s__Terrimonas sp002399735	76.4912	115	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720745.1	s__JJ008 sp016720745	76.4374	51	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.76	98.76	0.93	0.93	2	-
GCA_001898405.1	s__46-32 sp001898405	76.3811	64	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	98.21	96.99	0.89	0.84	4	-
GCF_007830055.1	s__Lacibacter cauensis	76.3794	85	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295245.1	s__JACMLD01 sp004295245	76.3765	61	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JACMLD01	95.0	98.79	98.79	0.91	0.91	2	-
GCA_002337125.1	s__Lacibacter sp002337125	76.3723	64	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744795.1	s__Niabella sp017744795	76.3444	95	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192765.1	s__Agriterribacter humi	76.3337	50	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288945.1	s__Puia sp013288945	76.3301	53	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	76.2163	90	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696395.1	s__MGR-bin208 sp013696395	75.7703	53	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__MGR-bin208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266575.1	s__Puia sp018266575	75.5576	67	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870685.1	s__CAILAF01 sp903870685	75.5199	61	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_005882975.1	s__VBAS01 sp005882975	75.3145	58	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:38,584] [INFO] GTDB search result was written to GCF_022513635.1_ASM2251363v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:38,584] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:38,588] [INFO] DFAST_QC result json was written to GCF_022513635.1_ASM2251363v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:38,588] [INFO] DFAST_QC completed!
[2024-01-25 19:47:38,588] [INFO] Total running time: 0h1m48s