[2023-03-15 17:46:31,616] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,617] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,617] [INFO] DQC Reference Directory: /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference
[2023-03-15 17:46:32,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,746] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,746] [INFO] Running command: cat /var/lib/cwl/stg65e4c09e-c1ef-45bd-9f69-b8d2825321eb/OceanDNA-b9636.fa | prodigal -d OceanDNA-b9636/cds.fna -a OceanDNA-b9636/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:41,962] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:41,962] [INFO] Task started: HMMsearch
[2023-03-15 17:46:41,963] [INFO] Running command: hmmsearch --tblout OceanDNA-b9636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/reference_markers.hmm OceanDNA-b9636/protein.faa > /dev/null
[2023-03-15 17:46:42,201] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:42,202] [INFO] Found 6/6 markers.
[2023-03-15 17:46:42,228] [INFO] Query marker FASTA was written to OceanDNA-b9636/markers.fasta
[2023-03-15 17:46:42,228] [INFO] Task started: Blastn
[2023-03-15 17:46:42,228] [INFO] Running command: blastn -query OceanDNA-b9636/markers.fasta -db /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/reference_markers.fasta -out OceanDNA-b9636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:42,922] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:42,926] [INFO] Selected 31 target genomes.
[2023-03-15 17:46:42,926] [INFO] Target genome list was writen to OceanDNA-b9636/target_genomes.txt
[2023-03-15 17:46:42,944] [INFO] Task started: fastANI
[2023-03-15 17:46:42,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e4c09e-c1ef-45bd-9f69-b8d2825321eb/OceanDNA-b9636.fa --refList OceanDNA-b9636/target_genomes.txt --output OceanDNA-b9636/fastani_result.tsv --threads 1
[2023-03-15 17:47:02,445] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:02,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:02,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:02,456] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:02,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:02,457] [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
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	77.1034	85	451	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.9896	81	451	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.9558	79	451	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.9374	78	451	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.9113	102	451	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.8962	81	451	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.8302	77	451	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.7961	103	451	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.7278	81	451	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	76.7268	98	451	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.6679	78	451	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.6191	91	451	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.5907	80	451	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	76.5288	63	451	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.4278	88	451	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.0999	71	451	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:02,458] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9636/tc_result.tsv
[2023-03-15 17:47:02,458] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:02,458] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:02,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/checkm_data
[2023-03-15 17:47:02,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:02,466] [INFO] Task started: CheckM
[2023-03-15 17:47:02,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9636/checkm_input OceanDNA-b9636/checkm_result
[2023-03-15 17:47:30,104] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:30,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:30,112] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:30,112] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:30,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9636/markers.fasta)
[2023-03-15 17:47:30,113] [INFO] Task started: Blastn
[2023-03-15 17:47:30,113] [INFO] Running command: blastn -query OceanDNA-b9636/markers.fasta -db /var/lib/cwl/stga282b93b-b946-4916-b59f-8f716dc0ab66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:31,126] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:31,130] [INFO] Selected 30 target genomes.
[2023-03-15 17:47:31,130] [INFO] Target genome list was writen to OceanDNA-b9636/target_genomes_gtdb.txt
[2023-03-15 17:47:31,161] [INFO] Task started: fastANI
[2023-03-15 17:47:31,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e4c09e-c1ef-45bd-9f69-b8d2825321eb/OceanDNA-b9636.fa --refList OceanDNA-b9636/target_genomes_gtdb.txt --output OceanDNA-b9636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:49,202] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:49,214] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:47:49,214] [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_004364175.1	s__Maribacter caenipelagi	77.1034	85	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	76.9896	81	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.9702	77	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112245.1	s__Maribacter stanieri	76.9361	101	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001447995.1	s__Maribacter dokdonensis	76.8962	81	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.891	102	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.8302	77	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	76.8195	102	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.7568	80	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCA_011050675.1	s__Maribacter sp011050675	76.7542	93	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018100785.1	s__Maribacter sp018100785	76.6948	57	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.6679	78	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	76.6437	90	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.6183	79	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.5976	99	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	76.5531	85	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.4278	88	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.4243	80	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144745.1	s__Croceivirga sp005144745	76.3218	50	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:49,216] [INFO] GTDB search result was written to OceanDNA-b9636/result_gtdb.tsv
[2023-03-15 17:47:49,217] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:49,220] [INFO] DFAST_QC result json was written to OceanDNA-b9636/dqc_result.json
[2023-03-15 17:47:49,220] [INFO] DFAST_QC completed!
[2023-03-15 17:47:49,220] [INFO] Total running time: 0h1m18s