[2024-01-24 11:34:41,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference
[2024-01-24 11:34:42,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,861] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,861] [INFO] Running command: gunzip -c /var/lib/cwl/stge17e104f-c236-4356-9ab0-9d586869258b/GCF_000746845.1_ASM74684v1_genomic.fna.gz | prodigal -d GCF_000746845.1_ASM74684v1_genomic.fna/cds.fna -a GCF_000746845.1_ASM74684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:58,303] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:58,303] [INFO] Task started: HMMsearch
[2024-01-24 11:34:58,304] [INFO] Running command: hmmsearch --tblout GCF_000746845.1_ASM74684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/reference_markers.hmm GCF_000746845.1_ASM74684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:58,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:58,566] [INFO] Found 6/6 markers.
[2024-01-24 11:34:58,605] [INFO] Query marker FASTA was written to GCF_000746845.1_ASM74684v1_genomic.fna/markers.fasta
[2024-01-24 11:34:58,606] [INFO] Task started: Blastn
[2024-01-24 11:34:58,606] [INFO] Running command: blastn -query GCF_000746845.1_ASM74684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/reference_markers.fasta -out GCF_000746845.1_ASM74684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:59,231] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:59,235] [INFO] Selected 25 target genomes.
[2024-01-24 11:34:59,235] [INFO] Target genome list was writen to GCF_000746845.1_ASM74684v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:59,244] [INFO] Task started: fastANI
[2024-01-24 11:34:59,244] [INFO] Running command: fastANI --query /var/lib/cwl/stge17e104f-c236-4356-9ab0-9d586869258b/GCF_000746845.1_ASM74684v1_genomic.fna.gz --refList GCF_000746845.1_ASM74684v1_genomic.fna/target_genomes.txt --output GCF_000746845.1_ASM74684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:16,274] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:16,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:16,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:16,287] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:16,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:16,287] [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
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	100.0	1048	1049	95	conclusive
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.416	167	1049	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	78.3828	56	1049	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.9039	225	1049	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.8263	134	1049	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.8014	134	1049	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.5395	143	1049	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.3806	62	1049	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	77.3047	93	1049	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.2706	135	1049	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.8747	60	1049	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	76.2324	50	1049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:16,291] [INFO] DFAST Taxonomy check result was written to GCF_000746845.1_ASM74684v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:16,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:16,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:16,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/checkm_data
[2024-01-24 11:35:16,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:16,344] [INFO] Task started: CheckM
[2024-01-24 11:35:16,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000746845.1_ASM74684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000746845.1_ASM74684v1_genomic.fna/checkm_input GCF_000746845.1_ASM74684v1_genomic.fna/checkm_result
[2024-01-24 11:36:00,933] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:00,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,953] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:00,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:00,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000746845.1_ASM74684v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:00,954] [INFO] Task started: Blastn
[2024-01-24 11:36:00,954] [INFO] Running command: blastn -query GCF_000746845.1_ASM74684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d95bda4-b5a1-408b-a5a3-14e35c598619/dqc_reference/reference_markers_gtdb.fasta -out GCF_000746845.1_ASM74684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:01,804] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:01,807] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:01,807] [INFO] Target genome list was writen to GCF_000746845.1_ASM74684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:01,821] [INFO] Task started: fastANI
[2024-01-24 11:36:01,821] [INFO] Running command: fastANI --query /var/lib/cwl/stge17e104f-c236-4356-9ab0-9d586869258b/GCF_000746845.1_ASM74684v1_genomic.fna.gz --refList GCF_000746845.1_ASM74684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000746845.1_ASM74684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:13,639] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:13,652] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:13,653] [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_000746845.1	s__Altibacter lentus	100.0	1048	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002696485.1	s__Altibacter sp002696485	84.4218	737	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	99.86	99.86	0.91	0.91	2	-
GCA_011044175.1	s__Marinirhabdus sp011044175	78.4795	132	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.4255	166	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	78.1182	286	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707025.1	s__IN17 sp002707025	78.0659	143	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	77.9743	192	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.8504	133	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.8286	135	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181835.1	s__GCA-002733185 sp905181835	77.5997	53	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476645.1	s__Aequorivita echinoideorum	77.3212	95	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.2706	135	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	77.1334	118	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043825.1	s__SMXJ01 sp013043825	77.0714	92	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043685.1	s__Pukyongia sp013043685	77.0049	101	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	-
GCA_002375695.1	s__Aequorivita sp002375695	76.8994	120	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.8619	114	1049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,654] [INFO] GTDB search result was written to GCF_000746845.1_ASM74684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:13,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:13,658] [INFO] DFAST_QC result json was written to GCF_000746845.1_ASM74684v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:13,658] [INFO] DFAST_QC completed!
[2024-01-24 11:36:13,658] [INFO] Total running time: 0h1m32s