[2023-03-18 03:45:10,275] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference
[2023-03-18 03:45:12,144] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,145] [INFO] Running command: cat /var/lib/cwl/stg6b7cd0d6-9cd7-4adb-bd82-7c16ab05f65d/OceanDNA-b10266.fa | prodigal -d OceanDNA-b10266/cds.fna -a OceanDNA-b10266/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:24,542] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:24,542] [INFO] Task started: HMMsearch
[2023-03-18 03:45:24,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b10266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/reference_markers.hmm OceanDNA-b10266/protein.faa > /dev/null
[2023-03-18 03:45:24,760] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:24,761] [INFO] Found 6/6 markers.
[2023-03-18 03:45:24,773] [INFO] Query marker FASTA was written to OceanDNA-b10266/markers.fasta
[2023-03-18 03:45:24,774] [INFO] Task started: Blastn
[2023-03-18 03:45:24,774] [INFO] Running command: blastn -query OceanDNA-b10266/markers.fasta -db /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/reference_markers.fasta -out OceanDNA-b10266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:25,351] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:25,352] [INFO] Selected 28 target genomes.
[2023-03-18 03:45:25,353] [INFO] Target genome list was writen to OceanDNA-b10266/target_genomes.txt
[2023-03-18 03:45:25,366] [INFO] Task started: fastANI
[2023-03-18 03:45:25,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7cd0d6-9cd7-4adb-bd82-7c16ab05f65d/OceanDNA-b10266.fa --refList OceanDNA-b10266/target_genomes.txt --output OceanDNA-b10266/fastani_result.tsv --threads 1
[2023-03-18 03:45:41,596] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:41,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:41,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:41,611] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:41,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:41,612] [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
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.9287	151	597	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.7389	135	597	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	76.7086	138	597	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.6859	114	597	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	76.6214	146	597	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.5829	145	597	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	76.5816	149	597	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.5691	128	597	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.5678	122	597	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.5474	126	597	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.5174	149	597	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.5028	127	597	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.4549	154	597	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.4449	142	597	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.3694	138	597	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.3616	165	597	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	76.3489	107	597	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.3393	102	597	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.2847	121	597	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.2637	106	597	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	76.2079	149	597	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.149	103	597	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.0482	123	597	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	75.9118	117	597	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	75.5742	63	597	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	75.5576	64	597	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:41,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10266/tc_result.tsv
[2023-03-18 03:45:41,612] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:41,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:41,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/checkm_data
[2023-03-18 03:45:41,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:41,629] [INFO] Task started: CheckM
[2023-03-18 03:45:41,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10266/checkm_input OceanDNA-b10266/checkm_result
[2023-03-18 03:46:17,661] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:17,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:17,664] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:17,664] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:17,664] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10266/markers.fasta)
[2023-03-18 03:46:17,665] [INFO] Task started: Blastn
[2023-03-18 03:46:17,665] [INFO] Running command: blastn -query OceanDNA-b10266/markers.fasta -db /var/lib/cwl/stg9c4aeccb-565b-4e40-893b-4859fe023b81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:18,486] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:18,487] [INFO] Selected 25 target genomes.
[2023-03-18 03:46:18,487] [INFO] Target genome list was writen to OceanDNA-b10266/target_genomes_gtdb.txt
[2023-03-18 03:46:18,610] [INFO] Task started: fastANI
[2023-03-18 03:46:18,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7cd0d6-9cd7-4adb-bd82-7c16ab05f65d/OceanDNA-b10266.fa --refList OceanDNA-b10266/target_genomes_gtdb.txt --output OceanDNA-b10266/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:31,863] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:31,875] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:31,875] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	78.0095	260	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	77.7028	266	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	77.5481	192	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	77.4499	196	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCF_001761365.1	s__Polaribacter vadi	76.7389	135	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018608545.1	s__Polaribacter sp018608545	76.7282	117	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	-
GCF_003335085.1	s__Polaribacter sp003335085	76.7099	123	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.6859	114	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.6805	153	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105455.1	s__Tenacibaculum sp900105455	76.6451	91	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	76.5816	149	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_013373385.1	s__Polaribacter_A sp013373385	76.539	99	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	76.5374	125	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	76.5028	127	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	76.5017	151	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.483	120	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_003129485.1	s__Polaribacter sp003129485	76.4672	153	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	76.4617	143	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	76.4449	142	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	76.4197	127	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCA_004762155.1	s__Tenacibaculum sp004762155	76.3005	118	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	75.9057	116	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:31,876] [INFO] GTDB search result was written to OceanDNA-b10266/result_gtdb.tsv
[2023-03-18 03:46:31,876] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:31,878] [INFO] DFAST_QC result json was written to OceanDNA-b10266/dqc_result.json
[2023-03-18 03:46:31,878] [INFO] DFAST_QC completed!
[2023-03-18 03:46:31,879] [INFO] Total running time: 0h1m22s