[2023-03-16 02:38:04,937] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference
[2023-03-16 02:38:06,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,128] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,128] [INFO] Running command: cat /var/lib/cwl/stg34d036f5-0397-466c-8d29-88b3d125deef/OceanDNA-b11418.fa | prodigal -d OceanDNA-b11418/cds.fna -a OceanDNA-b11418/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:20,920] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:20,921] [INFO] Task started: HMMsearch
[2023-03-16 02:38:20,921] [INFO] Running command: hmmsearch --tblout OceanDNA-b11418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/reference_markers.hmm OceanDNA-b11418/protein.faa > /dev/null
[2023-03-16 02:38:21,193] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:21,194] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg34d036f5-0397-466c-8d29-88b3d125deef/OceanDNA-b11418.fa]
[2023-03-16 02:38:21,211] [INFO] Query marker FASTA was written to OceanDNA-b11418/markers.fasta
[2023-03-16 02:38:21,211] [INFO] Task started: Blastn
[2023-03-16 02:38:21,211] [INFO] Running command: blastn -query OceanDNA-b11418/markers.fasta -db /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/reference_markers.fasta -out OceanDNA-b11418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:21,803] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:21,804] [INFO] Selected 18 target genomes.
[2023-03-16 02:38:21,804] [INFO] Target genome list was writen to OceanDNA-b11418/target_genomes.txt
[2023-03-16 02:38:21,814] [INFO] Task started: fastANI
[2023-03-16 02:38:21,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d036f5-0397-466c-8d29-88b3d125deef/OceanDNA-b11418.fa --refList OceanDNA-b11418/target_genomes.txt --output OceanDNA-b11418/fastani_result.tsv --threads 1
[2023-03-16 02:38:32,581] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:32,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:32,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:32,592] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:32,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:32,592] [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	79.8225	494	801	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	79.2769	473	801	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	79.0165	411	801	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1975	311	801	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1932	312	801	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.0225	309	801	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.6591	290	801	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.5407	245	801	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.5088	260	801	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.4519	246	801	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.2927	274	801	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.1848	186	801	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	77.0174	217	801	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9547	211	801	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8979	146	801	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.8519	180	801	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6398	138	801	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.3464	84	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:32,592] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11418/tc_result.tsv
[2023-03-16 02:38:32,592] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:32,592] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:32,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/checkm_data
[2023-03-16 02:38:32,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:32,598] [INFO] Task started: CheckM
[2023-03-16 02:38:32,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11418/checkm_input OceanDNA-b11418/checkm_result
[2023-03-16 02:39:12,243] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:12,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:12,246] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:12,246] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:12,246] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11418/markers.fasta)
[2023-03-16 02:39:12,247] [INFO] Task started: Blastn
[2023-03-16 02:39:12,247] [INFO] Running command: blastn -query OceanDNA-b11418/markers.fasta -db /var/lib/cwl/stg219be904-4191-4f65-852d-cf64976713d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:13,152] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:13,152] [INFO] Selected 9 target genomes.
[2023-03-16 02:39:13,153] [INFO] Target genome list was writen to OceanDNA-b11418/target_genomes_gtdb.txt
[2023-03-16 02:39:13,341] [INFO] Task started: fastANI
[2023-03-16 02:39:13,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg34d036f5-0397-466c-8d29-88b3d125deef/OceanDNA-b11418.fa --refList OceanDNA-b11418/target_genomes_gtdb.txt --output OceanDNA-b11418/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:18,816] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:18,822] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:18,822] [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_002163855.1	s__Winogradskyella sp002163855	99.9177	782	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	conclusive
GCA_905480385.1	s__Winogradskyella sp905480385	82.7174	489	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_013042245.1	s__Winogradskyella sp013042245	80.4563	394	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_004211785.1	s__Winogradskyella sp004211785	80.3826	486	801	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	79.8114	495	801	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	79.2777	473	801	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	79.0165	411	801	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	77.9078	302	801	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	77.8375	306	801	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:18,822] [INFO] GTDB search result was written to OceanDNA-b11418/result_gtdb.tsv
[2023-03-16 02:39:18,822] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:18,824] [INFO] DFAST_QC result json was written to OceanDNA-b11418/dqc_result.json
[2023-03-16 02:39:18,824] [INFO] DFAST_QC completed!
[2023-03-16 02:39:18,824] [INFO] Total running time: 0h1m14s