[2023-03-15 22:48:49,187] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:48:49,187] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:48:49,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference
[2023-03-15 22:48:50,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:48:50,295] [INFO] Task started: Prodigal
[2023-03-15 22:48:50,295] [INFO] Running command: cat /var/lib/cwl/stg16164776-4874-4865-a6d1-d9ffedfa7326/OceanDNA-b6196.fa | prodigal -d OceanDNA-b6196/cds.fna -a OceanDNA-b6196/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:49:11,294] [INFO] Task succeeded: Prodigal
[2023-03-15 22:49:11,294] [INFO] Task started: HMMsearch
[2023-03-15 22:49:11,294] [INFO] Running command: hmmsearch --tblout OceanDNA-b6196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/reference_markers.hmm OceanDNA-b6196/protein.faa > /dev/null
[2023-03-15 22:49:11,494] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:49:11,495] [INFO] Found 6/6 markers.
[2023-03-15 22:49:11,515] [INFO] Query marker FASTA was written to OceanDNA-b6196/markers.fasta
[2023-03-15 22:49:11,516] [INFO] Task started: Blastn
[2023-03-15 22:49:11,516] [INFO] Running command: blastn -query OceanDNA-b6196/markers.fasta -db /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/reference_markers.fasta -out OceanDNA-b6196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:12,118] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:12,118] [INFO] Selected 23 target genomes.
[2023-03-15 22:49:12,119] [INFO] Target genome list was writen to OceanDNA-b6196/target_genomes.txt
[2023-03-15 22:49:12,157] [INFO] Task started: fastANI
[2023-03-15 22:49:12,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg16164776-4874-4865-a6d1-d9ffedfa7326/OceanDNA-b6196.fa --refList OceanDNA-b6196/target_genomes.txt --output OceanDNA-b6196/fastani_result.tsv --threads 1
[2023-03-15 22:49:26,154] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:26,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:49:26,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:49:26,168] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:49:26,168] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:49:26,168] [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
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	77.3845	228	1059	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	77.1864	247	1059	95	below_threshold
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	77.0652	222	1059	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	77.0492	226	1059	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.8252	134	1059	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.746	119	1059	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	76.7206	135	1059	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.7114	152	1059	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.6709	120	1059	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.6382	130	1059	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.6072	64	1059	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.5789	143	1059	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	76.5568	104	1059	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.5471	127	1059	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	76.5174	130	1059	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	76.5127	121	1059	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.4847	129	1059	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.3568	144	1059	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.3452	156	1059	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	76.289	85	1059	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.2874	123	1059	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.2119	130	1059	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.058	135	1059	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:49:26,172] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6196/tc_result.tsv
[2023-03-15 22:49:26,173] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:49:26,173] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:49:26,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/checkm_data
[2023-03-15 22:49:26,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:49:26,178] [INFO] Task started: CheckM
[2023-03-15 22:49:26,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6196/checkm_input OceanDNA-b6196/checkm_result
[2023-03-15 22:50:19,406] [INFO] Task succeeded: CheckM
[2023-03-15 22:50:19,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:50:19,450] [INFO] ===== Completeness check finished =====
[2023-03-15 22:50:19,450] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:50:19,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6196/markers.fasta)
[2023-03-15 22:50:19,452] [INFO] Task started: Blastn
[2023-03-15 22:50:19,452] [INFO] Running command: blastn -query OceanDNA-b6196/markers.fasta -db /var/lib/cwl/stg9ab248c6-d98f-4dc4-a9f4-9a8348b59201/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:50:20,239] [INFO] Task succeeded: Blastn
[2023-03-15 22:50:20,284] [INFO] Selected 22 target genomes.
[2023-03-15 22:50:20,284] [INFO] Target genome list was writen to OceanDNA-b6196/target_genomes_gtdb.txt
[2023-03-15 22:50:20,855] [INFO] Task started: fastANI
[2023-03-15 22:50:20,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg16164776-4874-4865-a6d1-d9ffedfa7326/OceanDNA-b6196.fa --refList OceanDNA-b6196/target_genomes_gtdb.txt --output OceanDNA-b6196/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:50:34,561] [INFO] Task succeeded: fastANI
[2023-03-15 22:50:34,573] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:50:34,574] [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
GCF_003449015.1	s__Aureibaculum sp003449015	77.3975	227	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006065315.1	s__Aureibaculum sp006065315	77.1979	246	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	77.0652	222	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406085.1	s__Aureibaculum sp016406085	77.0373	227	1059	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	76.9887	118	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352665.1	s__Aureibaculum sp002352665	76.9535	223	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	76.8252	134	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330545.1	s__Aureibaculum sp011330545	76.8245	110	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	76.7215	136	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	76.6872	103	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_004121075.1	s__Lutibacter sp004121075	76.6615	132	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106565.1	s__Lutibacter oricola	76.6382	130	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	76.5568	104	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	76.5471	127	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013041805.1	s__Lutibacter sp013041805	76.5107	124	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012524075.1	s__Lutibacter sp012524075	76.4236	133	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337695.1	s__Tenacibaculum sp004337695	76.4174	113	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	76.3531	143	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390165.1	s__Lutibacter sp002390165	76.3105	92	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	76.2427	127	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	76.2119	130	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744615.1	s__QNYL01 sp016744615	75.9626	98	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QNYL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:50:34,625] [INFO] GTDB search result was written to OceanDNA-b6196/result_gtdb.tsv
[2023-03-15 22:50:34,626] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:50:34,628] [INFO] DFAST_QC result json was written to OceanDNA-b6196/dqc_result.json
[2023-03-15 22:50:34,628] [INFO] DFAST_QC completed!
[2023-03-15 22:50:34,628] [INFO] Total running time: 0h1m45s