[2023-03-18 05:27:36,798] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,798] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference
[2023-03-18 05:27:37,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:37,959] [INFO] Task started: Prodigal
[2023-03-18 05:27:37,959] [INFO] Running command: cat /var/lib/cwl/stge7cce941-63ae-4760-b93a-9fabf0831078/OceanDNA-b10690.fa | prodigal -d OceanDNA-b10690/cds.fna -a OceanDNA-b10690/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:27:49,560] [INFO] Task succeeded: Prodigal
[2023-03-18 05:27:49,561] [INFO] Task started: HMMsearch
[2023-03-18 05:27:49,561] [INFO] Running command: hmmsearch --tblout OceanDNA-b10690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/reference_markers.hmm OceanDNA-b10690/protein.faa > /dev/null
[2023-03-18 05:27:49,737] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:27:49,738] [INFO] Found 6/6 markers.
[2023-03-18 05:27:49,750] [INFO] Query marker FASTA was written to OceanDNA-b10690/markers.fasta
[2023-03-18 05:27:49,750] [INFO] Task started: Blastn
[2023-03-18 05:27:49,750] [INFO] Running command: blastn -query OceanDNA-b10690/markers.fasta -db /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/reference_markers.fasta -out OceanDNA-b10690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:27:50,305] [INFO] Task succeeded: Blastn
[2023-03-18 05:27:50,306] [INFO] Selected 38 target genomes.
[2023-03-18 05:27:50,306] [INFO] Target genome list was writen to OceanDNA-b10690/target_genomes.txt
[2023-03-18 05:27:50,322] [INFO] Task started: fastANI
[2023-03-18 05:27:50,323] [INFO] Running command: fastANI --query /var/lib/cwl/stge7cce941-63ae-4760-b93a-9fabf0831078/OceanDNA-b10690.fa --refList OceanDNA-b10690/target_genomes.txt --output OceanDNA-b10690/fastani_result.tsv --threads 1
[2023-03-18 05:28:12,926] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:12,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:28:12,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:28:12,937] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:28:12,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:28:12,938] [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
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.0124	60	539	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	77.0117	54	539	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.8961	63	539	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.7232	54	539	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.7069	53	539	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.6776	57	539	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.5626	59	539	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.5276	57	539	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.449	55	539	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.4051	57	539	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.3844	58	539	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	76.3531	51	539	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.2683	63	539	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.2449	63	539	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.1821	57	539	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.1714	67	539	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.1714	67	539	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.1714	67	539	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:28:12,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10690/tc_result.tsv
[2023-03-18 05:28:12,938] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:28:12,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:28:12,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/checkm_data
[2023-03-18 05:28:12,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:28:12,942] [INFO] Task started: CheckM
[2023-03-18 05:28:12,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10690/checkm_input OceanDNA-b10690/checkm_result
[2023-03-18 05:28:46,375] [INFO] Task succeeded: CheckM
[2023-03-18 05:28:46,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:28:46,412] [INFO] ===== Completeness check finished =====
[2023-03-18 05:28:46,413] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:28:46,413] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10690/markers.fasta)
[2023-03-18 05:28:46,414] [INFO] Task started: Blastn
[2023-03-18 05:28:46,414] [INFO] Running command: blastn -query OceanDNA-b10690/markers.fasta -db /var/lib/cwl/stg4f0ad08e-2667-4c28-a799-43751d3bf2c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:28:47,194] [INFO] Task succeeded: Blastn
[2023-03-18 05:28:47,195] [INFO] Selected 21 target genomes.
[2023-03-18 05:28:47,195] [INFO] Target genome list was writen to OceanDNA-b10690/target_genomes_gtdb.txt
[2023-03-18 05:28:47,211] [INFO] Task started: fastANI
[2023-03-18 05:28:47,211] [INFO] Running command: fastANI --query /var/lib/cwl/stge7cce941-63ae-4760-b93a-9fabf0831078/OceanDNA-b10690.fa --refList OceanDNA-b10690/target_genomes_gtdb.txt --output OceanDNA-b10690/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:28:55,969] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:55,980] [INFO] Found 19 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 05:28:55,980] [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_002684355.1	s__UBA3537 sp002684355	96.3176	425	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	inconclusive
GCA_002690085.1	s__UBA3537 sp002690085	96.1647	332	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002709185.1	s__UBA3537 sp002709185	90.0724	284	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_902516685.1	s__UBA3537 sp902516685	82.9993	146	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698705.1	s__UBA3537 sp002698705	82.5112	258	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	78.696	203	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCF_001735715.1	s__GCA001735715 sp001735715	78.2296	165	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_003144015.1	s__Xanthomarina sp003144015	77.0681	57	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	76.6776	57	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	76.664	54	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721175.1	s__SP29 sp002721175	76.5664	73	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SP29	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	76.5626	59	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.4082	83	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	76.2627	64	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.2136	76	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.1821	57	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.1714	67	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002784145.1	s__Yeosuana sp002784145	76.047	60	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	75.9985	86	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:28:55,980] [INFO] GTDB search result was written to OceanDNA-b10690/result_gtdb.tsv
[2023-03-18 05:28:55,980] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:28:55,982] [INFO] DFAST_QC result json was written to OceanDNA-b10690/dqc_result.json
[2023-03-18 05:28:55,982] [INFO] DFAST_QC completed!
[2023-03-18 05:28:55,982] [INFO] Total running time: 0h1m19s