[2023-03-16 21:45:15,291] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,291] [INFO] DQC Reference Directory: /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference
[2023-03-16 21:45:16,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,398] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,399] [INFO] Running command: cat /var/lib/cwl/stgc34b2a11-fcb8-4b24-bb31-25e0b16c0389/OceanDNA-b6653.fa | prodigal -d OceanDNA-b6653/cds.fna -a OceanDNA-b6653/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:30,404] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:30,404] [INFO] Task started: HMMsearch
[2023-03-16 21:45:30,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b6653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/reference_markers.hmm OceanDNA-b6653/protein.faa > /dev/null
[2023-03-16 21:45:30,624] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:30,625] [INFO] Found 6/6 markers.
[2023-03-16 21:45:30,639] [INFO] Query marker FASTA was written to OceanDNA-b6653/markers.fasta
[2023-03-16 21:45:30,639] [INFO] Task started: Blastn
[2023-03-16 21:45:30,639] [INFO] Running command: blastn -query OceanDNA-b6653/markers.fasta -db /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/reference_markers.fasta -out OceanDNA-b6653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:31,223] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:31,224] [INFO] Selected 23 target genomes.
[2023-03-16 21:45:31,225] [INFO] Target genome list was writen to OceanDNA-b6653/target_genomes.txt
[2023-03-16 21:45:31,235] [INFO] Task started: fastANI
[2023-03-16 21:45:31,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34b2a11-fcb8-4b24-bb31-25e0b16c0389/OceanDNA-b6653.fa --refList OceanDNA-b6653/target_genomes.txt --output OceanDNA-b6653/fastani_result.tsv --threads 1
[2023-03-16 21:45:44,216] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:44,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:44,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:44,228] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:44,228] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:44,228] [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
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.6357	136	699	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.5972	145	699	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.5965	156	699	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.5735	82	699	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.5676	92	699	95	below_threshold
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	76.4446	96	699	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.4278	80	699	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.3901	83	699	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.3791	85	699	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.3729	84	699	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.3611	94	699	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.3105	89	699	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.2899	115	699	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.2819	119	699	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.2701	79	699	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.259	80	699	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	76.2499	60	699	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	76.2288	66	699	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.2137	88	699	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.2113	103	699	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.0468	88	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:44,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6653/tc_result.tsv
[2023-03-16 21:45:44,229] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:44,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:44,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/checkm_data
[2023-03-16 21:45:44,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:44,235] [INFO] Task started: CheckM
[2023-03-16 21:45:44,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6653/checkm_input OceanDNA-b6653/checkm_result
[2023-03-16 21:46:22,086] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:22,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:22,089] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:22,089] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:22,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6653/markers.fasta)
[2023-03-16 21:46:22,090] [INFO] Task started: Blastn
[2023-03-16 21:46:22,090] [INFO] Running command: blastn -query OceanDNA-b6653/markers.fasta -db /var/lib/cwl/stge9d412f3-a16a-43de-8a74-efa4ff7734e3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:22,908] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:22,909] [INFO] Selected 24 target genomes.
[2023-03-16 21:46:22,909] [INFO] Target genome list was writen to OceanDNA-b6653/target_genomes_gtdb.txt
[2023-03-16 21:46:22,934] [INFO] Task started: fastANI
[2023-03-16 21:46:22,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34b2a11-fcb8-4b24-bb31-25e0b16c0389/OceanDNA-b6653.fa --refList OceanDNA-b6653/target_genomes_gtdb.txt --output OceanDNA-b6653/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:36,744] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:36,757] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:46:36,758] [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_013205245.1	s__CG1-02-35-72 sp013205245	99.1091	625	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CG1-02-35-72	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002793215.1	s__CG1-02-35-72 sp002793215	77.8495	268	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CG1-02-35-72	95.0	99.54	99.35	0.88	0.86	7	-
GCF_001761325.1	s__Urechidicola croceus	76.781	81	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	76.6357	136	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116115.1	s__Lutibacter maritimus	76.6209	154	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003449015.1	s__Aureibaculum sp003449015	76.5935	81	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.5872	118	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	76.541	96	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	76.4244	79	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	76.4233	97	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	76.4092	81	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006065315.1	s__Aureibaculum sp006065315	76.3791	85	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	76.3105	89	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201235.1	s__Polaribacter tangerinus	76.2775	59	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733285.1	s__Lutibacter sp002733285	76.2505	99	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.79	97.79	0.89	0.89	2	-
GCF_002163675.1	s__Polaribacter sp002163675	76.2479	85	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	76.2137	88	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	76.1629	70	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	76.1147	97	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	76.0641	87	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	76.0381	72	699	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	75.8124	55	699	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	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:36,758] [INFO] GTDB search result was written to OceanDNA-b6653/result_gtdb.tsv
[2023-03-16 21:46:36,758] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:36,760] [INFO] DFAST_QC result json was written to OceanDNA-b6653/dqc_result.json
[2023-03-16 21:46:36,760] [INFO] DFAST_QC completed!
[2023-03-16 21:46:36,760] [INFO] Total running time: 0h1m21s