[2024-01-25 20:05:05,519] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:05,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:05,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference
[2024-01-25 20:05:06,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:06,619] [INFO] Task started: Prodigal
[2024-01-25 20:05:06,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e0692a0-bd2b-4651-b2b6-48b400b3d16b/GCF_013294015.1_ASM1329401v1_genomic.fna.gz | prodigal -d GCF_013294015.1_ASM1329401v1_genomic.fna/cds.fna -a GCF_013294015.1_ASM1329401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:17,626] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:17,626] [INFO] Task started: HMMsearch
[2024-01-25 20:05:17,626] [INFO] Running command: hmmsearch --tblout GCF_013294015.1_ASM1329401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/reference_markers.hmm GCF_013294015.1_ASM1329401v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:17,839] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:17,840] [INFO] Found 6/6 markers.
[2024-01-25 20:05:17,866] [INFO] Query marker FASTA was written to GCF_013294015.1_ASM1329401v1_genomic.fna/markers.fasta
[2024-01-25 20:05:17,866] [INFO] Task started: Blastn
[2024-01-25 20:05:17,866] [INFO] Running command: blastn -query GCF_013294015.1_ASM1329401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/reference_markers.fasta -out GCF_013294015.1_ASM1329401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:18,449] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:18,452] [INFO] Selected 30 target genomes.
[2024-01-25 20:05:18,452] [INFO] Target genome list was writen to GCF_013294015.1_ASM1329401v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:18,483] [INFO] Task started: fastANI
[2024-01-25 20:05:18,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e0692a0-bd2b-4651-b2b6-48b400b3d16b/GCF_013294015.1_ASM1329401v1_genomic.fna.gz --refList GCF_013294015.1_ASM1329401v1_genomic.fna/target_genomes.txt --output GCF_013294015.1_ASM1329401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:36,826] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:36,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:36,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:36,841] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:36,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:36,842] [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
Frigoriflavimonas asaccharolytica	strain=16F	GCA_013294015.1	2735899	2735899	type	True	100.0	1105	1108	95	conclusive
Halpernia frigidisoli	strain=DSM 26000	GCA_900113805.1	1125876	1125876	type	True	77.5189	236	1108	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	77.467	206	1108	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	77.4027	229	1108	95	below_threshold
Halpernia humi	strain=DSM 21580	GCA_900108025.1	493375	493375	type	True	77.3768	266	1108	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.1452	174	1108	95	below_threshold
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	76.857	184	1108	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	76.8393	168	1108	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	76.7614	169	1108	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	76.7459	191	1108	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	76.7157	172	1108	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	76.7031	115	1108	95	below_threshold
Chryseobacterium defluvii	strain=DSM 14219	GCA_003634775.1	160396	160396	type	True	76.6718	107	1108	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	76.6697	194	1108	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	76.6286	192	1108	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	76.6264	119	1108	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	76.6156	117	1108	95	below_threshold
Chryseobacterium balustinum	strain=NCTC11212	GCA_900446785.1	246	246	type	True	76.595	175	1108	95	below_threshold
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	76.5809	186	1108	95	below_threshold
Epilithonimonas caeni	strain=DSM 17710	GCA_000426465.1	365343	365343	type	True	76.4308	101	1108	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	76.4106	131	1108	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.0125	54	1108	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.8956	72	1108	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.6268	66	1108	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.5673	66	1108	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.5073	73	1108	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.4662	61	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:36,843] [INFO] DFAST Taxonomy check result was written to GCF_013294015.1_ASM1329401v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:36,843] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:36,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:36,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/checkm_data
[2024-01-25 20:05:36,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:36,880] [INFO] Task started: CheckM
[2024-01-25 20:05:36,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013294015.1_ASM1329401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013294015.1_ASM1329401v1_genomic.fna/checkm_input GCF_013294015.1_ASM1329401v1_genomic.fna/checkm_result
[2024-01-25 20:06:10,970] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:10,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:10,993] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:10,993] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:10,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013294015.1_ASM1329401v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:10,994] [INFO] Task started: Blastn
[2024-01-25 20:06:10,994] [INFO] Running command: blastn -query GCF_013294015.1_ASM1329401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bf79fd9-b9d5-45d6-885c-7fd05ada0574/dqc_reference/reference_markers_gtdb.fasta -out GCF_013294015.1_ASM1329401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:11,847] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:11,850] [INFO] Selected 25 target genomes.
[2024-01-25 20:06:11,850] [INFO] Target genome list was writen to GCF_013294015.1_ASM1329401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:11,919] [INFO] Task started: fastANI
[2024-01-25 20:06:11,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e0692a0-bd2b-4651-b2b6-48b400b3d16b/GCF_013294015.1_ASM1329401v1_genomic.fna.gz --refList GCF_013294015.1_ASM1329401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013294015.1_ASM1329401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:27,803] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:27,816] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:27,817] [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_013294015.1	s__Halpernia sp013294015	100.0	1105	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113805.1	s__Halpernia frigidisoli	77.5023	238	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679325.1	s__Kaistella gelatinilytica	77.467	206	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812865.1	s__Kaistella jeonii	77.4557	224	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900108025.1	s__Halpernia humi	77.3793	265	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Halpernia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860585.1	s__Kaistella carnis	77.1307	175	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_907163125.1	s__Cloacibacterium caeni_B	77.1084	206	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_014645495.1	s__Cloacibacterium rupense	76.8699	183	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745795.1	s__Chryseobacterium sp000745795	76.8009	198	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017808115.1	s__Chryseobacterium sp017808115	76.7772	158	1108	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	76.7712	110	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156685.1	s__Chryseobacterium piscicola	76.7475	170	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_903166575.1	s__Chryseobacterium sp903166575	76.7247	173	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	76.723	193	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_016595215.1	s__Chryseobacterium sp016595215	76.7031	115	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634775.1	s__Chryseobacterium defluvii	76.6718	107	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168205.1	s__Chryseobacterium balustinum	76.5695	187	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.96	99.93	0.98	0.95	3	-
GCF_002216065.1	s__Chryseobacterium sp002216065	76.5171	130	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430825.1	s__Chryseobacterium daeguense	76.4106	131	1108	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	76.3847	158	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045455.1	s__Chryseobacterium sp001045455	76.3395	136	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058315.1	s__Soonwooa sp011058315	76.3315	132	1108	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Soonwooa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:27,818] [INFO] GTDB search result was written to GCF_013294015.1_ASM1329401v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:27,819] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:27,823] [INFO] DFAST_QC result json was written to GCF_013294015.1_ASM1329401v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:27,823] [INFO] DFAST_QC completed!
[2024-01-25 20:06:27,823] [INFO] Total running time: 0h1m22s