[2023-03-19 05:32:20,810] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:32:20,810] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:32:20,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference
[2023-03-19 05:32:22,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:32:22,380] [INFO] Task started: Prodigal
[2023-03-19 05:32:22,381] [INFO] Running command: cat /var/lib/cwl/stg51de953b-4e51-4d2e-9901-a357c9e0cc73/OceanDNA-b11388.fa | prodigal -d OceanDNA-b11388/cds.fna -a OceanDNA-b11388/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:32:42,815] [INFO] Task succeeded: Prodigal
[2023-03-19 05:32:42,815] [INFO] Task started: HMMsearch
[2023-03-19 05:32:42,815] [INFO] Running command: hmmsearch --tblout OceanDNA-b11388/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/reference_markers.hmm OceanDNA-b11388/protein.faa > /dev/null
[2023-03-19 05:32:43,019] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:32:43,020] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51de953b-4e51-4d2e-9901-a357c9e0cc73/OceanDNA-b11388.fa]
[2023-03-19 05:32:43,040] [INFO] Query marker FASTA was written to OceanDNA-b11388/markers.fasta
[2023-03-19 05:32:43,040] [INFO] Task started: Blastn
[2023-03-19 05:32:43,040] [INFO] Running command: blastn -query OceanDNA-b11388/markers.fasta -db /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/reference_markers.fasta -out OceanDNA-b11388/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:32:43,611] [INFO] Task succeeded: Blastn
[2023-03-19 05:32:43,612] [INFO] Selected 18 target genomes.
[2023-03-19 05:32:43,612] [INFO] Target genome list was writen to OceanDNA-b11388/target_genomes.txt
[2023-03-19 05:32:43,621] [INFO] Task started: fastANI
[2023-03-19 05:32:43,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg51de953b-4e51-4d2e-9901-a357c9e0cc73/OceanDNA-b11388.fa --refList OceanDNA-b11388/target_genomes.txt --output OceanDNA-b11388/fastani_result.tsv --threads 1
[2023-03-19 05:32:55,431] [INFO] Task succeeded: fastANI
[2023-03-19 05:32:55,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:32:55,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:32:55,442] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:32:55,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:32:55,442] [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 echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.2329	550	1096	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.2155	552	1096	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	79.1546	517	1096	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.9622	485	1096	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.9222	516	1096	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.8512	472	1096	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	78.8466	495	1096	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.7971	448	1096	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.587	467	1096	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.456	422	1096	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.4281	412	1096	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.3615	446	1096	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.0553	395	1096	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.7758	161	1096	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.7051	162	1096	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6222	163	1096	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.057	119	1096	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	75.8669	83	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:32:55,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11388/tc_result.tsv
[2023-03-19 05:32:55,443] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:32:55,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:32:55,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/checkm_data
[2023-03-19 05:32:55,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:32:55,448] [INFO] Task started: CheckM
[2023-03-19 05:32:55,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11388/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11388/checkm_input OceanDNA-b11388/checkm_result
[2023-03-19 05:33:47,072] [INFO] Task succeeded: CheckM
[2023-03-19 05:33:47,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:33:47,075] [INFO] ===== Completeness check finished =====
[2023-03-19 05:33:47,075] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:33:47,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11388/markers.fasta)
[2023-03-19 05:33:47,076] [INFO] Task started: Blastn
[2023-03-19 05:33:47,076] [INFO] Running command: blastn -query OceanDNA-b11388/markers.fasta -db /var/lib/cwl/stg2be6b57d-64ca-434f-9c31-2554dac41162/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11388/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:33:47,832] [INFO] Task succeeded: Blastn
[2023-03-19 05:33:47,832] [INFO] Selected 12 target genomes.
[2023-03-19 05:33:47,833] [INFO] Target genome list was writen to OceanDNA-b11388/target_genomes_gtdb.txt
[2023-03-19 05:33:47,841] [INFO] Task started: fastANI
[2023-03-19 05:33:47,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg51de953b-4e51-4d2e-9901-a357c9e0cc73/OceanDNA-b11388.fa --refList OceanDNA-b11388/target_genomes_gtdb.txt --output OceanDNA-b11388/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:33:56,975] [INFO] Task succeeded: fastANI
[2023-03-19 05:33:56,982] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:33:56,982] [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_002364335.1	s__Winogradskyella sp002364335	81.9684	590	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	81.2316	634	1096	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	79.5678	557	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	79.1618	517	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	79.1061	515	1096	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	79.0776	551	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	78.9875	483	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.9356	497	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	78.9303	515	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	78.6625	466	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	78.6048	431	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_013249045.1	s__Winogradskyella eckloniae	78.4281	412	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:33:56,983] [INFO] GTDB search result was written to OceanDNA-b11388/result_gtdb.tsv
[2023-03-19 05:33:56,983] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:33:56,984] [INFO] DFAST_QC result json was written to OceanDNA-b11388/dqc_result.json
[2023-03-19 05:33:56,985] [INFO] DFAST_QC completed!
[2023-03-19 05:33:56,985] [INFO] Total running time: 0h1m36s