[2024-01-24 13:49:45,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference
[2024-01-24 13:49:46,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,957] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,958] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8a2b034-badc-4ea1-882a-41ff6a90f08d/GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/cds.fna -a GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:00,478] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:00,478] [INFO] Task started: HMMsearch
[2024-01-24 13:50:00,478] [INFO] Running command: hmmsearch --tblout GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/reference_markers.hmm GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:00,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:00,780] [INFO] Found 6/6 markers.
[2024-01-24 13:50:00,819] [INFO] Query marker FASTA was written to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:00,820] [INFO] Task started: Blastn
[2024-01-24 13:50:00,820] [INFO] Running command: blastn -query GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/reference_markers.fasta -out GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,489] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:01,490] [INFO] Target genome list was writen to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,500] [INFO] Task started: fastANI
[2024-01-24 13:50:01,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a2b034-badc-4ea1-882a-41ff6a90f08d/GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna.gz --refList GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:18,268] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:18,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:18,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:18,288] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:18,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:18,289] [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
Soonwooa buanensis	strain=DSM 22323	GCA_900167905.1	619805	619805	type	True	100.0	1097	1097	95	conclusive
Epilithonimonas vandammei	strain=F5649	GCA_003860525.1	2487072	2487072	type	True	78.0484	231	1097	95	below_threshold
Epilithonimonas hispanica	strain=KCTC 22104	GCA_003385395.1	358687	358687	type	True	77.9662	261	1097	95	below_threshold
Epilithonimonas arachidiradicis	strain=DSM 27620	GCA_003610695.1	1617282	1617282	type	True	77.8948	246	1097	95	below_threshold
Epilithonimonas arachidiradicis	strain=CCM 8490	GCA_014635405.1	1617282	1617282	type	True	77.8562	248	1097	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	77.8531	273	1097	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	77.8275	217	1097	95	below_threshold
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	77.8142	134	1097	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.7676	185	1097	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	77.7669	245	1097	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	77.7625	205	1097	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	77.7124	219	1097	95	below_threshold
Epilithonimonas xixisoli	strain=CGMCC 1.12802	GCA_004365655.1	1476462	1476462	type	True	77.7102	243	1097	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	77.6388	193	1097	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	77.594	237	1097	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.5266	229	1097	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	77.4523	164	1097	95	below_threshold
Chryseobacterium gallinarum	strain=DSM 27622	GCA_001021975.1	1324352	1324352	type	True	77.3798	138	1097	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	77.36	140	1097	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	76.8833	142	1097	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	76.8434	141	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:18,291] [INFO] DFAST Taxonomy check result was written to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:18,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:18,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:18,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/checkm_data
[2024-01-24 13:50:18,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:18,329] [INFO] Task started: CheckM
[2024-01-24 13:50:18,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/checkm_input GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:59,566] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:59,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:59,590] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:59,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:59,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:59,591] [INFO] Task started: Blastn
[2024-01-24 13:50:59,592] [INFO] Running command: blastn -query GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg54dd4297-b347-4bc2-a4dd-812473077ca3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,440] [INFO] Selected 23 target genomes.
[2024-01-24 13:51:00,440] [INFO] Target genome list was writen to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,469] [INFO] Task started: fastANI
[2024-01-24 13:51:00,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a2b034-badc-4ea1-882a-41ff6a90f08d/GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna.gz --refList GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:14,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:14,613] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:14,614] [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_900167905.1	s__Soonwooa buanensis	100.0	1097	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Soonwooa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011058315.1	s__Soonwooa sp011058315	81.4767	628	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Soonwooa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345565.1	s__Epilithonimonas sp002345565	78.1645	255	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860525.1	s__Epilithonimonas vandammei	78.0665	231	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.28	95.86	0.86	0.84	4	-
GCF_003860565.1	s__Cloacibacterium normanense	77.9573	185	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	98.41	95.23	0.95	0.87	4	-
GCF_003610695.1	s__Epilithonimonas arachidiradicis	77.8961	246	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385415.1	s__Chryseobacterium piscium	77.8269	217	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	-
GCF_014779605.1	s__Chryseobacterium sp014779605	77.8192	224	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_003730015.1	s__Epilithonimonas hominis	77.7824	215	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.55	96.42	0.86	0.85	3	-
GCF_004365655.1	s__Epilithonimonas xixisoli	77.7231	242	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383165.1	s__Epilithonimonas sp002383165	77.7172	235	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163125.1	s__Cloacibacterium caeni_B	77.7029	190	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.1075	N/A	N/A	N/A	N/A	1	-
GCF_002943105.1	s__Cloacibacterium sp002422665	77.5125	185	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0662	95.27	95.25	0.87	0.85	3	-
GCF_903166575.1	s__Chryseobacterium sp903166575	77.5	231	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099685.1	s__Chryseobacterium taeanense	77.4626	165	1097	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	77.4528	217	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799195.1	s__Chryseobacterium sp000799195	77.433	219	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927325.1	s__Chryseobacterium antibioticum	77.36	140	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735135.1	s__Epilithonimonas sp000735135	77.2792	231	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989575.1	s__Epilithonimonas sp017989575	77.2158	174	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015191005.1	s__Kaistella flava	77.0133	177	1097	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	77.0037	135	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337005.1	s__Cloacibacterium sp002337005	77.0004	160	1097	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 13:51:14,616] [INFO] GTDB search result was written to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:14,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:14,621] [INFO] DFAST_QC result json was written to GCF_900167905.1_IMG-taxon_2595698221_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:14,621] [INFO] DFAST_QC completed!
[2024-01-24 13:51:14,621] [INFO] Total running time: 0h1m29s