[2024-01-24 13:41:20,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference
[2024-01-24 13:41:21,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,921] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,922] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3e9b187-12e7-4a29-820a-ff29048d1ff9/GCF_014235875.1_ASM1423587v1_genomic.fna.gz | prodigal -d GCF_014235875.1_ASM1423587v1_genomic.fna/cds.fna -a GCF_014235875.1_ASM1423587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:34,083] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:34,084] [INFO] Task started: HMMsearch
[2024-01-24 13:41:34,084] [INFO] Running command: hmmsearch --tblout GCF_014235875.1_ASM1423587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/reference_markers.hmm GCF_014235875.1_ASM1423587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:34,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:34,366] [INFO] Found 6/6 markers.
[2024-01-24 13:41:34,399] [INFO] Query marker FASTA was written to GCF_014235875.1_ASM1423587v1_genomic.fna/markers.fasta
[2024-01-24 13:41:34,406] [INFO] Task started: Blastn
[2024-01-24 13:41:34,407] [INFO] Running command: blastn -query GCF_014235875.1_ASM1423587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/reference_markers.fasta -out GCF_014235875.1_ASM1423587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,127] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:35,128] [INFO] Target genome list was writen to GCF_014235875.1_ASM1423587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:35,136] [INFO] Task started: fastANI
[2024-01-24 13:41:35,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e9b187-12e7-4a29-820a-ff29048d1ff9/GCF_014235875.1_ASM1423587v1_genomic.fna.gz --refList GCF_014235875.1_ASM1423587v1_genomic.fna/target_genomes.txt --output GCF_014235875.1_ASM1423587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,126] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:50,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,127] [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
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	100.0	1140	1141	95	conclusive
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	99.9977	1137	1141	95	conclusive
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	77.885	248	1141	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.9475	185	1141	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.8472	131	1141	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.7175	198	1141	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.6353	169	1141	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.6232	62	1141	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.5952	162	1141	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.5878	128	1141	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.571	127	1141	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.5535	130	1141	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.5174	100	1141	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.226	110	1141	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.1845	100	1141	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	76.1809	100	1141	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.1267	108	1141	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.1251	84	1141	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.1124	115	1141	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.0312	69	1141	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.8612	87	1141	95	below_threshold
Psychroflexus salarius	strain=DSM 25661	GCA_900129035.1	1155689	1155689	type	True	75.7665	62	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,133] [INFO] DFAST Taxonomy check result was written to GCF_014235875.1_ASM1423587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/checkm_data
[2024-01-24 13:41:50,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,188] [INFO] Task started: CheckM
[2024-01-24 13:41:50,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014235875.1_ASM1423587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014235875.1_ASM1423587v1_genomic.fna/checkm_input GCF_014235875.1_ASM1423587v1_genomic.fna/checkm_result
[2024-01-24 13:42:27,676] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:27,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:27,698] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:27,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:27,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014235875.1_ASM1423587v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:27,699] [INFO] Task started: Blastn
[2024-01-24 13:42:27,700] [INFO] Running command: blastn -query GCF_014235875.1_ASM1423587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f857f0c-ad7b-4ada-a115-49a4ba26bb76/dqc_reference/reference_markers_gtdb.fasta -out GCF_014235875.1_ASM1423587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:28,607] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:28,615] [INFO] Selected 25 target genomes.
[2024-01-24 13:42:28,615] [INFO] Target genome list was writen to GCF_014235875.1_ASM1423587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:28,633] [INFO] Task started: fastANI
[2024-01-24 13:42:28,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e9b187-12e7-4a29-820a-ff29048d1ff9/GCF_014235875.1_ASM1423587v1_genomic.fna.gz --refList GCF_014235875.1_ASM1423587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014235875.1_ASM1423587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:43,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:43,280] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:43,281] [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_014235875.1	s__Croceivirga lutea	100.0	1140	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005144745.1	s__Croceivirga sp005144745	78.8876	262	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_002072105.2	s__Croceivirga radicis	77.885	248	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.98	97.98	0.93	0.93	2	-
GCF_004364175.1	s__Maribacter caenipelagi	77.1425	164	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272815.1	s__Croceivirga sp012272815	77.0286	213	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.8476	130	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.7311	189	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.7175	198	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	76.664	101	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCA_016744255.1	s__Maribacter_B sp016744255	76.6255	155	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.608	160	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.5998	188	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.5878	128	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.5034	158	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.4241	156	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_900114265.1	s__Flaviramulus basaltis	76.3261	136	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349235.1	s__Euzebyella sp014349235	76.3217	93	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141885.1	s__Mesonia phycicola	76.2073	111	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	76.1125	115	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	76.0211	68	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000967805.1	s__Flavobacterium sp000967805	75.8405	89	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129035.1	s__Psychroflexus salarius	75.7665	62	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964435.1	s__Mesonia sp012964435	75.515	65	1141	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:43,282] [INFO] GTDB search result was written to GCF_014235875.1_ASM1423587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:43,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:43,290] [INFO] DFAST_QC result json was written to GCF_014235875.1_ASM1423587v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:43,290] [INFO] DFAST_QC completed!
[2024-01-24 13:42:43,291] [INFO] Total running time: 0h1m23s