[2024-01-24 12:14:35,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,502] [INFO] DQC Reference Directory: /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference
[2024-01-24 12:14:36,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,794] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgabeeb8a4-f2fa-4479-aceb-a4d4a061bbed/GCF_003095375.1_ASM309537v1_genomic.fna.gz | prodigal -d GCF_003095375.1_ASM309537v1_genomic.fna/cds.fna -a GCF_003095375.1_ASM309537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:53,790] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:53,791] [INFO] Task started: HMMsearch
[2024-01-24 12:14:53,791] [INFO] Running command: hmmsearch --tblout GCF_003095375.1_ASM309537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/reference_markers.hmm GCF_003095375.1_ASM309537v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:54,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:54,092] [INFO] Found 6/6 markers.
[2024-01-24 12:14:54,125] [INFO] Query marker FASTA was written to GCF_003095375.1_ASM309537v1_genomic.fna/markers.fasta
[2024-01-24 12:14:54,125] [INFO] Task started: Blastn
[2024-01-24 12:14:54,126] [INFO] Running command: blastn -query GCF_003095375.1_ASM309537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/reference_markers.fasta -out GCF_003095375.1_ASM309537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:54,766] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:54,769] [INFO] Selected 21 target genomes.
[2024-01-24 12:14:54,770] [INFO] Target genome list was writen to GCF_003095375.1_ASM309537v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:54,779] [INFO] Task started: fastANI
[2024-01-24 12:14:54,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgabeeb8a4-f2fa-4479-aceb-a4d4a061bbed/GCF_003095375.1_ASM309537v1_genomic.fna.gz --refList GCF_003095375.1_ASM309537v1_genomic.fna/target_genomes.txt --output GCF_003095375.1_ASM309537v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:07,287] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:07,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:07,310] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:07,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:07,310] [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
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	100.0	1118	1119	95	conclusive
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	80.4306	615	1119	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	77.1697	182	1119	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.0813	95	1119	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	77.0297	182	1119	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	77.0088	169	1119	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.9088	189	1119	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.8877	116	1119	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.7902	150	1119	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.7673	146	1119	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.7071	172	1119	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6439	140	1119	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.6406	137	1119	95	below_threshold
Salegentibacter sediminis	strain=K5023	GCA_002078605.1	1930251	1930251	type	True	76.6296	54	1119	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5344	50	1119	95	below_threshold
Mangrovimonas yunxiaonensis	strain=LY01	GCA_000733475.1	1197477	1197477	type	True	76.4871	72	1119	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.3276	53	1119	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.2346	56	1119	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	76.2328	70	1119	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.1923	67	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,312] [INFO] DFAST Taxonomy check result was written to GCF_003095375.1_ASM309537v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:07,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:07,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:07,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/checkm_data
[2024-01-24 12:15:07,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:07,348] [INFO] Task started: CheckM
[2024-01-24 12:15:07,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003095375.1_ASM309537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003095375.1_ASM309537v1_genomic.fna/checkm_input GCF_003095375.1_ASM309537v1_genomic.fna/checkm_result
[2024-01-24 12:15:56,098] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:56,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,127] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:56,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:56,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003095375.1_ASM309537v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:56,128] [INFO] Task started: Blastn
[2024-01-24 12:15:56,129] [INFO] Running command: blastn -query GCF_003095375.1_ASM309537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5d17082-5d57-40d5-af4f-a05da98be1eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003095375.1_ASM309537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:56,973] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:56,976] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:56,976] [INFO] Target genome list was writen to GCF_003095375.1_ASM309537v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:56,989] [INFO] Task started: fastANI
[2024-01-24 12:15:56,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgabeeb8a4-f2fa-4479-aceb-a4d4a061bbed/GCF_003095375.1_ASM309537v1_genomic.fna.gz --refList GCF_003095375.1_ASM309537v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003095375.1_ASM309537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:06,037] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:06,053] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:06,053] [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_003095375.1	s__Marixanthomonas sp003095375	100.0	1118	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002360635.1	s__Marixanthomonas sp002360635	80.7796	635	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002364245.1	s__Marixanthomonas sp002364245	80.6568	392	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	80.4306	615	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	80.2987	617	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	77.2603	146	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	77.1697	182	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966125.1	s__Pukyongia salina	77.1249	85	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	77.1075	94	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	77.0281	181	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	76.9955	170	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_905479745.1	s__Pukyongia sp905479745	76.8782	67	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707745.1	s__Marinirhabdus sp002707745	76.861	105	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCF_007997135.1	s__Aequorivita lipolytica	76.7492	146	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002707025.1	s__IN17 sp002707025	76.745	127	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCF_007997155.1	s__Aequorivita antarctica	76.7071	172	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002375695.1	s__Aequorivita sp002375695	76.6007	138	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:06,056] [INFO] GTDB search result was written to GCF_003095375.1_ASM309537v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:06,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:06,061] [INFO] DFAST_QC result json was written to GCF_003095375.1_ASM309537v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:06,061] [INFO] DFAST_QC completed!
[2024-01-24 12:16:06,061] [INFO] Total running time: 0h1m31s