[2023-03-18 05:17:48,239] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:17:48,239] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:17:48,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference
[2023-03-18 05:17:49,337] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:17:49,337] [INFO] Task started: Prodigal
[2023-03-18 05:17:49,337] [INFO] Running command: cat /var/lib/cwl/stgdf576888-2aa2-43eb-af2e-c4abeaef56ca/OceanDNA-b11385.fa | prodigal -d OceanDNA-b11385/cds.fna -a OceanDNA-b11385/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:18:07,361] [INFO] Task succeeded: Prodigal
[2023-03-18 05:18:07,362] [INFO] Task started: HMMsearch
[2023-03-18 05:18:07,362] [INFO] Running command: hmmsearch --tblout OceanDNA-b11385/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/reference_markers.hmm OceanDNA-b11385/protein.faa > /dev/null
[2023-03-18 05:18:07,559] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:18:07,560] [INFO] Found 6/6 markers.
[2023-03-18 05:18:07,579] [INFO] Query marker FASTA was written to OceanDNA-b11385/markers.fasta
[2023-03-18 05:18:07,581] [INFO] Task started: Blastn
[2023-03-18 05:18:07,581] [INFO] Running command: blastn -query OceanDNA-b11385/markers.fasta -db /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/reference_markers.fasta -out OceanDNA-b11385/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:18:08,200] [INFO] Task succeeded: Blastn
[2023-03-18 05:18:08,202] [INFO] Selected 28 target genomes.
[2023-03-18 05:18:08,202] [INFO] Target genome list was writen to OceanDNA-b11385/target_genomes.txt
[2023-03-18 05:18:08,223] [INFO] Task started: fastANI
[2023-03-18 05:18:08,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf576888-2aa2-43eb-af2e-c4abeaef56ca/OceanDNA-b11385.fa --refList OceanDNA-b11385/target_genomes.txt --output OceanDNA-b11385/fastani_result.tsv --threads 1
[2023-03-18 05:18:23,484] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:23,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:18:23,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:18:23,498] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:18:23,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:18:23,499] [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
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.0689	209	941	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.0689	209	941	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.0168	160	941	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.9492	183	941	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.9446	189	941	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.7955	187	941	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.735	142	941	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.7034	122	941	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.6819	153	941	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.5689	66	941	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.5499	158	941	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5024	117	941	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.3987	54	941	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.3609	75	941	95	below_threshold
Winogradskyella aurantiaca	strain=IMCC20180	GCA_003362725.1	2219558	2219558	type	True	76.3308	96	941	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.2872	114	941	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.285	161	941	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.1879	162	941	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.1059	95	941	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.0268	81	941	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	75.999	87	941	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	75.9688	123	941	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	75.9243	85	941	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	75.7997	91	941	95	below_threshold
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	75.7379	53	941	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:18:23,500] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11385/tc_result.tsv
[2023-03-18 05:18:23,500] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:18:23,500] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:18:23,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/checkm_data
[2023-03-18 05:18:23,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:18:23,636] [INFO] Task started: CheckM
[2023-03-18 05:18:23,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11385/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11385/checkm_input OceanDNA-b11385/checkm_result
[2023-03-18 05:19:10,237] [INFO] Task succeeded: CheckM
[2023-03-18 05:19:10,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:19:10,287] [INFO] ===== Completeness check finished =====
[2023-03-18 05:19:10,287] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:19:10,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11385/markers.fasta)
[2023-03-18 05:19:10,289] [INFO] Task started: Blastn
[2023-03-18 05:19:10,289] [INFO] Running command: blastn -query OceanDNA-b11385/markers.fasta -db /var/lib/cwl/stgaf508546-c499-444e-afbb-1e3e158ed308/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11385/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:19:11,154] [INFO] Task succeeded: Blastn
[2023-03-18 05:19:11,158] [INFO] Selected 27 target genomes.
[2023-03-18 05:19:11,158] [INFO] Target genome list was writen to OceanDNA-b11385/target_genomes_gtdb.txt
[2023-03-18 05:19:11,208] [INFO] Task started: fastANI
[2023-03-18 05:19:11,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf576888-2aa2-43eb-af2e-c4abeaef56ca/OceanDNA-b11385.fa --refList OceanDNA-b11385/target_genomes_gtdb.txt --output OceanDNA-b11385/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:19:25,809] [INFO] Task succeeded: fastANI
[2023-03-18 05:19:25,823] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:19:25,824] [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_002722255.1	s__Winogradskyella sp002722255	77.0647	154	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_014297365.1	s__Winogradskyella echinorum	77.0602	208	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129745.1	s__Winogradskyella jejuensis	77.0183	159	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002225.1	s__Winogradskyella sp013002225	76.8941	128	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712105.1	s__Winogradskyella sp003712105	76.8872	169	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	76.8432	227	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.8235	195	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.7955	187	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.757	164	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.735	142	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260205.1	s__Winogradskyella tangerina	76.709	172	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	76.6819	153	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211785.1	s__Winogradskyella sp004211785	76.6437	172	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706045.1	s__Winogradskyella sp002706045	76.5577	127	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	76.5429	129	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	76.5387	110	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	76.5257	228	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	76.4394	168	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874335.1	s__MedPE-SWsnd-G2 sp001874335	76.3932	106	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	76.3666	76	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCA_003443635.1	s__AU392 sp003443635	76.3539	137	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003362725.1	s__Winogradskyella aurantiaca	76.3308	96	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	76.329	86	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	76.1993	86	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006148925.1	s__Algibacter_D aestuarii	76.0245	87	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042715.1	s__Site-B15 sp013042715	75.9761	75	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	75.7997	91	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:19:25,825] [INFO] GTDB search result was written to OceanDNA-b11385/result_gtdb.tsv
[2023-03-18 05:19:25,826] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:19:25,831] [INFO] DFAST_QC result json was written to OceanDNA-b11385/dqc_result.json
[2023-03-18 05:19:25,831] [INFO] DFAST_QC completed!
[2023-03-18 05:19:25,831] [INFO] Total running time: 0h1m38s