[2023-03-14 11:49:16,958] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:16,961] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:16,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference
[2023-03-14 11:49:18,050] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:18,051] [INFO] Task started: Prodigal
[2023-03-14 11:49:18,051] [INFO] Running command: cat /var/lib/cwl/stg1b0810a3-4171-42a4-a765-0d7661ad5b6d/OceanDNA-b11360.fa | prodigal -d OceanDNA-b11360/cds.fna -a OceanDNA-b11360/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:31,287] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:31,288] [INFO] Task started: HMMsearch
[2023-03-14 11:49:31,288] [INFO] Running command: hmmsearch --tblout OceanDNA-b11360/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/reference_markers.hmm OceanDNA-b11360/protein.faa > /dev/null
[2023-03-14 11:49:31,474] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:31,475] [INFO] Found 6/6 markers.
[2023-03-14 11:49:31,508] [INFO] Query marker FASTA was written to OceanDNA-b11360/markers.fasta
[2023-03-14 11:49:31,509] [INFO] Task started: Blastn
[2023-03-14 11:49:31,509] [INFO] Running command: blastn -query OceanDNA-b11360/markers.fasta -db /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/reference_markers.fasta -out OceanDNA-b11360/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:32,112] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:32,116] [INFO] Selected 17 target genomes.
[2023-03-14 11:49:32,116] [INFO] Target genome list was writen to OceanDNA-b11360/target_genomes.txt
[2023-03-14 11:49:32,125] [INFO] Task started: fastANI
[2023-03-14 11:49:32,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0810a3-4171-42a4-a765-0d7661ad5b6d/OceanDNA-b11360.fa --refList OceanDNA-b11360/target_genomes.txt --output OceanDNA-b11360/fastani_result.tsv --threads 1
[2023-03-14 11:49:41,983] [INFO] Task succeeded: fastANI
[2023-03-14 11:49:41,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:49:41,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:49:41,994] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:49:41,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:49:41,994] [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 haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	79.807	494	719	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	79.1864	459	719	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	78.8998	412	719	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1864	314	719	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1864	314	719	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.0851	270	719	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.9144	237	719	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.8616	256	719	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.8046	262	719	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.7787	288	719	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.7687	269	719	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.568	190	719	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.2833	135	719	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9244	155	719	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.8127	110	719	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.7679	170	719	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.726	86	719	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:49:42,006] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11360/tc_result.tsv
[2023-03-14 11:49:42,028] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:49:42,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:49:42,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/checkm_data
[2023-03-14 11:49:42,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:49:42,035] [INFO] Task started: CheckM
[2023-03-14 11:49:42,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11360/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11360/checkm_input OceanDNA-b11360/checkm_result
[2023-03-14 11:50:18,566] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:18,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:18,680] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:18,680] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:18,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11360/markers.fasta)
[2023-03-14 11:50:18,681] [INFO] Task started: Blastn
[2023-03-14 11:50:18,681] [INFO] Running command: blastn -query OceanDNA-b11360/markers.fasta -db /var/lib/cwl/stgaf6d3e0b-5138-43e0-af7d-4d054bf5bd86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11360/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:19,554] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:19,560] [INFO] Selected 10 target genomes.
[2023-03-14 11:50:19,560] [INFO] Target genome list was writen to OceanDNA-b11360/target_genomes_gtdb.txt
[2023-03-14 11:50:19,583] [INFO] Task started: fastANI
[2023-03-14 11:50:19,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0810a3-4171-42a4-a765-0d7661ad5b6d/OceanDNA-b11360.fa --refList OceanDNA-b11360/target_genomes_gtdb.txt --output OceanDNA-b11360/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:50:25,615] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:25,621] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:50:25,622] [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_905480385.1	s__Winogradskyella sp905480385	99.6358	599	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	conclusive
GCF_002163855.1	s__Winogradskyella sp002163855	83.1245	612	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_004211785.1	s__Winogradskyella sp004211785	80.2972	462	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	80.0139	385	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_014635865.1	s__Winogradskyella haliclonae	79.807	494	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	79.1864	459	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	78.8998	412	719	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	78.3343	293	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.0565	313	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.5373	285	719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:50:25,625] [INFO] GTDB search result was written to OceanDNA-b11360/result_gtdb.tsv
[2023-03-14 11:50:25,631] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:50:25,637] [INFO] DFAST_QC result json was written to OceanDNA-b11360/dqc_result.json
[2023-03-14 11:50:25,637] [INFO] DFAST_QC completed!
[2023-03-14 11:50:25,637] [INFO] Total running time: 0h1m9s