[2023-06-17 16:58:59,610] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:59,612] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:59,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference
[2023-06-17 16:59:00,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:59:00,904] [INFO] Task started: Prodigal
[2023-06-17 16:59:00,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg44c8c0b7-3708-4d99-9d5c-6b8c8bfa6de1/GCA_009995175.1_ASM999517v1_genomic.fna.gz | prodigal -d GCA_009995175.1_ASM999517v1_genomic.fna/cds.fna -a GCA_009995175.1_ASM999517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:59:11,831] [INFO] Task succeeded: Prodigal
[2023-06-17 16:59:11,831] [INFO] Task started: HMMsearch
[2023-06-17 16:59:11,831] [INFO] Running command: hmmsearch --tblout GCA_009995175.1_ASM999517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/reference_markers.hmm GCA_009995175.1_ASM999517v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:59:12,167] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:59:12,169] [INFO] Found 6/6 markers.
[2023-06-17 16:59:12,201] [INFO] Query marker FASTA was written to GCA_009995175.1_ASM999517v1_genomic.fna/markers.fasta
[2023-06-17 16:59:12,201] [INFO] Task started: Blastn
[2023-06-17 16:59:12,201] [INFO] Running command: blastn -query GCA_009995175.1_ASM999517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/reference_markers.fasta -out GCA_009995175.1_ASM999517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:12,873] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:12,877] [INFO] Selected 30 target genomes.
[2023-06-17 16:59:12,878] [INFO] Target genome list was writen to GCA_009995175.1_ASM999517v1_genomic.fna/target_genomes.txt
[2023-06-17 16:59:12,888] [INFO] Task started: fastANI
[2023-06-17 16:59:12,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c8c0b7-3708-4d99-9d5c-6b8c8bfa6de1/GCA_009995175.1_ASM999517v1_genomic.fna.gz --refList GCA_009995175.1_ASM999517v1_genomic.fna/target_genomes.txt --output GCA_009995175.1_ASM999517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:31,201] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:31,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:31,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:31,221] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:31,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:59:31,222] [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
Planktosalinus lacus	strain=CGMCC 1.12924	GCA_014640155.1	1526573	1526573	type	True	76.9752	192	867	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	76.7957	55	867	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6536	94	867	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.6103	93	867	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.5843	72	867	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.4542	73	867	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.4226	70	867	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.4143	65	867	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.4031	78	867	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.3279	96	867	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.2934	78	867	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	76.1791	60	867	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.1433	75	867	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0549	77	867	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.0122	51	867	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.9984	83	867	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.9881	82	867	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	75.8725	96	867	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	75.8604	65	867	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	75.7885	62	867	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	75.7272	62	867	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.6407	83	867	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.4766	79	867	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	75.4433	75	867	95	below_threshold
Flavobacterium branchiophilum	strain=ATCC 35035	GCA_002217205.1	55197	55197	type	True	75.4142	64	867	95	below_threshold
Flavobacterium branchiophilum	strain=NBRC 15030	GCA_007990815.1	55197	55197	type	True	75.3926	65	867	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	75.37	67	867	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:59:31,224] [INFO] DFAST Taxonomy check result was written to GCA_009995175.1_ASM999517v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:31,225] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:31,225] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:31,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/checkm_data
[2023-06-17 16:59:31,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:31,257] [INFO] Task started: CheckM
[2023-06-17 16:59:31,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009995175.1_ASM999517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009995175.1_ASM999517v1_genomic.fna/checkm_input GCA_009995175.1_ASM999517v1_genomic.fna/checkm_result
[2023-06-17 17:00:06,080] [INFO] Task succeeded: CheckM
[2023-06-17 17:00:06,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 17:00:06,106] [INFO] ===== Completeness check finished =====
[2023-06-17 17:00:06,106] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:00:06,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009995175.1_ASM999517v1_genomic.fna/markers.fasta)
[2023-06-17 17:00:06,107] [INFO] Task started: Blastn
[2023-06-17 17:00:06,107] [INFO] Running command: blastn -query GCA_009995175.1_ASM999517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92ecb9aa-f9b0-4f06-ae2f-e59caa7eff59/dqc_reference/reference_markers_gtdb.fasta -out GCA_009995175.1_ASM999517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:00:06,990] [INFO] Task succeeded: Blastn
[2023-06-17 17:00:06,995] [INFO] Selected 21 target genomes.
[2023-06-17 17:00:06,996] [INFO] Target genome list was writen to GCA_009995175.1_ASM999517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:00:07,007] [INFO] Task started: fastANI
[2023-06-17 17:00:07,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c8c0b7-3708-4d99-9d5c-6b8c8bfa6de1/GCA_009995175.1_ASM999517v1_genomic.fna.gz --refList GCA_009995175.1_ASM999517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009995175.1_ASM999517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:00:18,847] [INFO] Task succeeded: fastANI
[2023-06-17 17:00:18,866] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 17:00:18,867] [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
GCA_001873105.1	s__Planktosalinus sp001873105	99.6884	713	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	99.77	99.69	0.89	0.85	7	conclusive
GCA_002842575.1	s__Planktosalinus sp002842575	85.5223	673	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402385.1	s__Planktosalinus sp018402385	77.3541	199	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640155.1	s__Planktosalinus lacus	76.9746	192	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.6103	93	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.5424	66	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.511	72	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	76.4542	73	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.3804	81	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	76.317	94	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000265385.1	s__Aequorivita sublithincola	76.3079	97	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997155.1	s__Aequorivita antarctica	76.2934	78	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014638915.1	s__Xanthomarina arctica	76.2538	89	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490835.1	s__GCA-002733185 sp015490835	76.1721	87	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	76.172	91	867	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_900114265.1	s__Flaviramulus basaltis	76.1365	88	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.0916	114	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.0607	99	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	75.8855	53	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_007489275.1	s__Aquimarina algiphila	75.7235	67	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-17 17:00:18,869] [INFO] GTDB search result was written to GCA_009995175.1_ASM999517v1_genomic.fna/result_gtdb.tsv
[2023-06-17 17:00:18,869] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:00:18,874] [INFO] DFAST_QC result json was written to GCA_009995175.1_ASM999517v1_genomic.fna/dqc_result.json
[2023-06-17 17:00:18,874] [INFO] DFAST_QC completed!
[2023-06-17 17:00:18,874] [INFO] Total running time: 0h1m19s