[2024-01-25 18:56:20,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference
[2024-01-25 18:56:21,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,712] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b848a99-8885-42cf-b4c0-fef68c3a0103/GCF_003852705.1_ASM385270v1_genomic.fna.gz | prodigal -d GCF_003852705.1_ASM385270v1_genomic.fna/cds.fna -a GCF_003852705.1_ASM385270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:32,040] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:32,040] [INFO] Task started: HMMsearch
[2024-01-25 18:56:32,040] [INFO] Running command: hmmsearch --tblout GCF_003852705.1_ASM385270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/reference_markers.hmm GCF_003852705.1_ASM385270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:32,268] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:32,269] [INFO] Found 6/6 markers.
[2024-01-25 18:56:32,293] [INFO] Query marker FASTA was written to GCF_003852705.1_ASM385270v1_genomic.fna/markers.fasta
[2024-01-25 18:56:32,293] [INFO] Task started: Blastn
[2024-01-25 18:56:32,293] [INFO] Running command: blastn -query GCF_003852705.1_ASM385270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/reference_markers.fasta -out GCF_003852705.1_ASM385270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:32,875] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:32,878] [INFO] Selected 23 target genomes.
[2024-01-25 18:56:32,878] [INFO] Target genome list was writen to GCF_003852705.1_ASM385270v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:32,893] [INFO] Task started: fastANI
[2024-01-25 18:56:32,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b848a99-8885-42cf-b4c0-fef68c3a0103/GCF_003852705.1_ASM385270v1_genomic.fna.gz --refList GCF_003852705.1_ASM385270v1_genomic.fna/target_genomes.txt --output GCF_003852705.1_ASM385270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:47,778] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:47,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:47,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:47,792] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:47,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:47,792] [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
Amniculibacterium aquaticum	strain=KYPW7	GCA_003852705.1	2479858	2479858	type	True	100.0	814	815	95	conclusive
Chryseobacterium taklimakanense	strain=NCTC13490	GCA_900187185.1	536441	536441	type	True	78.1544	103	815	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	78.0297	105	815	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.9493	117	815	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	77.8531	124	815	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	77.8051	124	815	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	77.6428	113	815	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	77.6035	135	815	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	77.5911	119	815	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	77.5783	119	815	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	77.5304	133	815	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	77.521	117	815	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_003860565.1	237258	237258	type	True	77.4915	160	815	95	below_threshold
Cloacibacterium normanense	strain=DSM 15886	GCA_900104195.1	237258	237258	type	True	77.4736	157	815	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_003815775.1	112234	112234	type	True	77.4591	109	815	95	below_threshold
Cloacibacterium normanense	strain=NRS-1	GCA_001747495.1	237258	237258	type	True	77.4208	154	815	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	77.405	90	815	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	77.394	112	815	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	77.3874	128	815	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	77.3871	146	815	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_900156585.1	112234	112234	type	True	77.3847	109	815	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	77.1508	113	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:47,807] [INFO] DFAST Taxonomy check result was written to GCF_003852705.1_ASM385270v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:47,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:47,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:47,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/checkm_data
[2024-01-25 18:56:47,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:47,838] [INFO] Task started: CheckM
[2024-01-25 18:56:47,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003852705.1_ASM385270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003852705.1_ASM385270v1_genomic.fna/checkm_input GCF_003852705.1_ASM385270v1_genomic.fna/checkm_result
[2024-01-25 18:57:20,857] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:20,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:20,875] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:20,875] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:20,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003852705.1_ASM385270v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:20,875] [INFO] Task started: Blastn
[2024-01-25 18:57:20,875] [INFO] Running command: blastn -query GCF_003852705.1_ASM385270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b1dd9ca-f1fe-4a6f-93b1-9ac8a7729c85/dqc_reference/reference_markers_gtdb.fasta -out GCF_003852705.1_ASM385270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:21,741] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:21,744] [INFO] Selected 24 target genomes.
[2024-01-25 18:57:21,744] [INFO] Target genome list was writen to GCF_003852705.1_ASM385270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:21,767] [INFO] Task started: fastANI
[2024-01-25 18:57:21,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b848a99-8885-42cf-b4c0-fef68c3a0103/GCF_003852705.1_ASM385270v1_genomic.fna.gz --refList GCF_003852705.1_ASM385270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003852705.1_ASM385270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:36,631] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:36,646] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:36,646] [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_003852705.1	s__Amniculibacterium aquaticum	100.0	814	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Amniculibacterium	95.0	98.89	98.89	0.92	0.92	2	conclusive
GCA_018266955.1	s__Amniculibacterium sp018266955	79.2491	371	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Amniculibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266965.1	s__Amniculibacterium sp018266965	78.6746	294	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Amniculibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187185.1	s__Planobacterium taklimakanense	78.1543	103	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Planobacterium	95.0	96.53	96.28	0.85	0.83	3	-
GCF_012927265.1	s__Chryseobacterium cheonjiense	77.9877	107	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	77.9441	91	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636535.1	s__Chryseobacterium gleum	77.7769	122	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.52	97.29	0.95	0.89	6	-
GCF_907163125.1	s__Cloacibacterium caeni_B	77.7277	146	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCA_015999765.1	s__Kaistella sp015999765	77.7139	89	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCA_019236175.1	s__Chryseobacterium sp019236175	77.7137	117	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	77.7094	129	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403755.1	s__Kaistella senegalense	77.6503	138	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163105.1	s__Cloacibacterium caeni_A	77.6285	132	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426785.1	s__Kaistella sp002426785	77.6215	122	815	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	77.5583	102	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116415.1	s__Chryseobacterium formosense	77.5069	134	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCF_003860565.1	s__Cloacibacterium normanense	77.4726	160	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	98.41	95.23	0.95	0.87	4	-
GCF_002943105.1	s__Cloacibacterium sp002422665	77.4463	140	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0662	95.27	95.25	0.87	0.85	3	-
GCF_000282115.1	s__Chryseobacterium populi	77.4067	120	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900111495.1	s__Chryseobacterium wanjuense	77.3858	146	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815655.1	s__Chryseobacterium sp003815655	77.3742	133	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	77.3201	132	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216065.1	s__Chryseobacterium sp002216065	77.2508	108	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184525.1	s__Chryseobacterium sp013184525	77.2364	119	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:36,647] [INFO] GTDB search result was written to GCF_003852705.1_ASM385270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:36,648] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:36,652] [INFO] DFAST_QC result json was written to GCF_003852705.1_ASM385270v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:36,652] [INFO] DFAST_QC completed!
[2024-01-25 18:57:36,652] [INFO] Total running time: 0h1m16s