[2023-03-18 05:27:36,800] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:27:36,801] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:27:36,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference
[2023-03-18 05:27:37,960] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:27:37,961] [INFO] Task started: Prodigal
[2023-03-18 05:27:37,961] [INFO] Running command: cat /var/lib/cwl/stgbfef38ba-512b-4186-a19b-2d8d3f3cf2cc/OceanDNA-b7450.fa | prodigal -d OceanDNA-b7450/cds.fna -a OceanDNA-b7450/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:28:13,094] [INFO] Task succeeded: Prodigal
[2023-03-18 05:28:13,094] [INFO] Task started: HMMsearch
[2023-03-18 05:28:13,094] [INFO] Running command: hmmsearch --tblout OceanDNA-b7450/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/reference_markers.hmm OceanDNA-b7450/protein.faa > /dev/null
[2023-03-18 05:28:13,330] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:28:13,330] [INFO] Found 6/6 markers.
[2023-03-18 05:28:13,356] [INFO] Query marker FASTA was written to OceanDNA-b7450/markers.fasta
[2023-03-18 05:28:13,357] [INFO] Task started: Blastn
[2023-03-18 05:28:13,357] [INFO] Running command: blastn -query OceanDNA-b7450/markers.fasta -db /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/reference_markers.fasta -out OceanDNA-b7450/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:28:13,895] [INFO] Task succeeded: Blastn
[2023-03-18 05:28:13,896] [INFO] Selected 28 target genomes.
[2023-03-18 05:28:13,897] [INFO] Target genome list was writen to OceanDNA-b7450/target_genomes.txt
[2023-03-18 05:28:13,915] [INFO] Task started: fastANI
[2023-03-18 05:28:13,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfef38ba-512b-4186-a19b-2d8d3f3cf2cc/OceanDNA-b7450.fa --refList OceanDNA-b7450/target_genomes.txt --output OceanDNA-b7450/fastani_result.tsv --threads 1
[2023-03-18 05:28:32,693] [INFO] Task succeeded: fastANI
[2023-03-18 05:28:32,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:28:32,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:28:32,708] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:28:32,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:28:32,709] [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
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.9024	205	1453	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.6601	148	1453	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	76.4554	109	1453	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.4019	150	1453	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.3633	150	1453	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	76.3388	137	1453	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.2853	80	1453	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.2719	121	1453	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	76.2466	93	1453	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.1994	116	1453	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	76.1858	113	1453	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.1831	131	1453	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.1798	136	1453	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.171	58	1453	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.1647	63	1453	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.0809	109	1453	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.0809	109	1453	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.0784	88	1453	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	76.0714	142	1453	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	76.0674	113	1453	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.0551	123	1453	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	75.9626	69	1453	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.9528	64	1453	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	75.8689	69	1453	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	75.7901	74	1453	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	75.469	81	1453	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:28:32,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7450/tc_result.tsv
[2023-03-18 05:28:32,727] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:28:32,727] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:28:32,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/checkm_data
[2023-03-18 05:28:32,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:28:32,746] [INFO] Task started: CheckM
[2023-03-18 05:28:32,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7450/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7450/checkm_input OceanDNA-b7450/checkm_result
[2023-03-18 05:29:57,700] [INFO] Task succeeded: CheckM
[2023-03-18 05:29:57,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:29:57,730] [INFO] ===== Completeness check finished =====
[2023-03-18 05:29:57,730] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:29:57,730] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7450/markers.fasta)
[2023-03-18 05:29:57,731] [INFO] Task started: Blastn
[2023-03-18 05:29:57,731] [INFO] Running command: blastn -query OceanDNA-b7450/markers.fasta -db /var/lib/cwl/stg7821166f-f9b2-4636-8a9e-94084c3c11b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7450/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:29:58,505] [INFO] Task succeeded: Blastn
[2023-03-18 05:29:58,517] [INFO] Selected 28 target genomes.
[2023-03-18 05:29:58,517] [INFO] Target genome list was writen to OceanDNA-b7450/target_genomes_gtdb.txt
[2023-03-18 05:29:58,595] [INFO] Task started: fastANI
[2023-03-18 05:29:58,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfef38ba-512b-4186-a19b-2d8d3f3cf2cc/OceanDNA-b7450.fa --refList OceanDNA-b7450/target_genomes_gtdb.txt --output OceanDNA-b7450/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:30:17,540] [INFO] Task succeeded: fastANI
[2023-03-18 05:30:17,555] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:30:17,555] [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_009371985.2	s__TP-CH-4 sp009371985	76.9024	205	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TP-CH-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005943945.1	s__F202Z8 sp005943945	76.6601	148	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__F202Z8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188415.1	s__Maribacter sedimenticola	76.5044	103	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_000153165.2	s__Maribacter_A sp000153165	76.5014	92	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	76.4554	109	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.4014	150	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_900156625.1	s__Zobellia uliginosa	76.3516	136	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001430825.1	s__Sediminicola sp001430825	76.3277	123	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	76.2853	80	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_900129275.1	s__Arenibacter palladensis	76.2719	121	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_015330165.1	s__Zobellia sp015330165	76.2466	93	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_900177645.1	s__Arenibacter troitsensis	76.1994	116	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	76.1952	127	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426735.1	s__Arenibacter sp003426735	76.1918	118	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	76.1885	134	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	76.1711	114	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424985.1	s__Arenibacter latericius	76.171	58	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	76.1647	63	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	76.1646	130	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.1254	154	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.0954	87	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626755.1	s__Ulvibacterium marinum	76.0714	142	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	76.0551	123	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.0286	74	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	75.9626	69	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_900129665.1	s__Muricauda flava	75.8065	73	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	75.5616	75	1453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:30:17,562] [INFO] GTDB search result was written to OceanDNA-b7450/result_gtdb.tsv
[2023-03-18 05:30:17,562] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:30:17,565] [INFO] DFAST_QC result json was written to OceanDNA-b7450/dqc_result.json
[2023-03-18 05:30:17,565] [INFO] DFAST_QC completed!
[2023-03-18 05:30:17,565] [INFO] Total running time: 0h2m41s