[2023-03-15 22:25:05,848] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:25:05,849] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:25:05,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference
[2023-03-15 22:25:06,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:25:06,951] [INFO] Task started: Prodigal
[2023-03-15 22:25:06,951] [INFO] Running command: cat /var/lib/cwl/stgdd1436c0-60df-424b-b731-4b5e4faa04eb/OceanDNA-b26636.fa | prodigal -d OceanDNA-b26636/cds.fna -a OceanDNA-b26636/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:25:32,989] [INFO] Task succeeded: Prodigal
[2023-03-15 22:25:32,990] [INFO] Task started: HMMsearch
[2023-03-15 22:25:32,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b26636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/reference_markers.hmm OceanDNA-b26636/protein.faa > /dev/null
[2023-03-15 22:25:33,210] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:25:33,210] [INFO] Found 6/6 markers.
[2023-03-15 22:25:33,240] [INFO] Query marker FASTA was written to OceanDNA-b26636/markers.fasta
[2023-03-15 22:25:33,240] [INFO] Task started: Blastn
[2023-03-15 22:25:33,240] [INFO] Running command: blastn -query OceanDNA-b26636/markers.fasta -db /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/reference_markers.fasta -out OceanDNA-b26636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:34,068] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:34,069] [INFO] Selected 18 target genomes.
[2023-03-15 22:25:34,069] [INFO] Target genome list was writen to OceanDNA-b26636/target_genomes.txt
[2023-03-15 22:25:34,079] [INFO] Task started: fastANI
[2023-03-15 22:25:34,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1436c0-60df-424b-b731-4b5e4faa04eb/OceanDNA-b26636.fa --refList OceanDNA-b26636/target_genomes.txt --output OceanDNA-b26636/fastani_result.tsv --threads 1
[2023-03-15 22:25:49,207] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:49,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:25:49,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:25:49,218] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:25:49,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:25:49,218] [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
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	81.6344	951	1379	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	81.5188	897	1379	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	81.4633	1005	1379	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.2255	585	1379	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3928	195	1379	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.3237	221	1379	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2729	154	1379	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.2633	153	1379	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1352	309	1379	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1069	312	1379	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	75.9721	128	1379	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	75.7795	127	1379	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	75.7735	129	1379	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6356	101	1379	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	75.6214	70	1379	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	75.6063	69	1379	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.5825	110	1379	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	75.4496	76	1379	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:25:49,219] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26636/tc_result.tsv
[2023-03-15 22:25:49,219] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:25:49,219] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:25:49,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/checkm_data
[2023-03-15 22:25:49,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:25:49,225] [INFO] Task started: CheckM
[2023-03-15 22:25:49,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26636/checkm_input OceanDNA-b26636/checkm_result
[2023-03-15 22:26:52,301] [INFO] Task succeeded: CheckM
[2023-03-15 22:26:52,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:26:52,305] [INFO] ===== Completeness check finished =====
[2023-03-15 22:26:52,305] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:26:52,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26636/markers.fasta)
[2023-03-15 22:26:52,306] [INFO] Task started: Blastn
[2023-03-15 22:26:52,306] [INFO] Running command: blastn -query OceanDNA-b26636/markers.fasta -db /var/lib/cwl/stg4de73307-96fb-487b-ab99-01bb5f45ca6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:26:54,073] [INFO] Task succeeded: Blastn
[2023-03-15 22:26:54,075] [INFO] Selected 20 target genomes.
[2023-03-15 22:26:54,075] [INFO] Target genome list was writen to OceanDNA-b26636/target_genomes_gtdb.txt
[2023-03-15 22:26:54,141] [INFO] Task started: fastANI
[2023-03-15 22:26:54,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1436c0-60df-424b-b731-4b5e4faa04eb/OceanDNA-b26636.fa --refList OceanDNA-b26636/target_genomes_gtdb.txt --output OceanDNA-b26636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:27:16,138] [INFO] Task succeeded: fastANI
[2023-03-15 22:27:16,149] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:27:16,150] [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_004296935.1	s__Reyranella sp004296935	84.7713	1068	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767945.1	s__Reyranella sp001767945	84.4613	927	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191685.1	s__Reyranella sp016191685	84.1158	765	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	83.4358	858	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	82.2432	740	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	81.9578	936	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	81.9535	836	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039055.1	s__Reyranella sp019039055	81.8147	968	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	81.7552	1020	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290035.1	s__Reyranella sp013290035	81.7414	585	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297265.1	s__Reyranella sp004297265	81.7277	940	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	81.719	955	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_900110395.1	s__Reyranella sp900110395	81.6974	1009	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772935.1	s__Reyranella sp009772935	81.6	954	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153415.1	s__Reyranella sp003153415	81.4044	817	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990895.1	s__Reyranella sp017990895	81.3757	764	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897995.1	s__Reyranella sp001897995	81.3438	836	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.19	98.73	0.86	0.86	3	-
GCA_018240695.1	s__Reyranella sp018240695	81.309	740	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_005884705.1	s__Reyranella sp005884705	81.0443	614	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832005.1	s__Reyranella aerosaccus_B	80.8212	834	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-15 22:27:16,151] [INFO] GTDB search result was written to OceanDNA-b26636/result_gtdb.tsv
[2023-03-15 22:27:16,151] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:27:16,154] [INFO] DFAST_QC result json was written to OceanDNA-b26636/dqc_result.json
[2023-03-15 22:27:16,154] [INFO] DFAST_QC completed!
[2023-03-15 22:27:16,154] [INFO] Total running time: 0h2m10s