[2023-03-16 12:01:18,302] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:01:18,302] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:01:18,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference
[2023-03-16 12:01:21,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:01:21,511] [INFO] Task started: Prodigal
[2023-03-16 12:01:21,511] [INFO] Running command: cat /var/lib/cwl/stg3c839058-820f-4e7c-a0f6-bd55b868977a/OceanDNA-b9722.fa | prodigal -d OceanDNA-b9722/cds.fna -a OceanDNA-b9722/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:01:32,486] [INFO] Task succeeded: Prodigal
[2023-03-16 12:01:32,486] [INFO] Task started: HMMsearch
[2023-03-16 12:01:32,486] [INFO] Running command: hmmsearch --tblout OceanDNA-b9722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/reference_markers.hmm OceanDNA-b9722/protein.faa > /dev/null
[2023-03-16 12:01:32,713] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:01:32,714] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3c839058-820f-4e7c-a0f6-bd55b868977a/OceanDNA-b9722.fa]
[2023-03-16 12:01:32,727] [INFO] Query marker FASTA was written to OceanDNA-b9722/markers.fasta
[2023-03-16 12:01:32,728] [INFO] Task started: Blastn
[2023-03-16 12:01:32,728] [INFO] Running command: blastn -query OceanDNA-b9722/markers.fasta -db /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/reference_markers.fasta -out OceanDNA-b9722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:01:35,876] [INFO] Task succeeded: Blastn
[2023-03-16 12:01:35,877] [INFO] Selected 17 target genomes.
[2023-03-16 12:01:35,877] [INFO] Target genome list was writen to OceanDNA-b9722/target_genomes.txt
[2023-03-16 12:01:35,888] [INFO] Task started: fastANI
[2023-03-16 12:01:35,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c839058-820f-4e7c-a0f6-bd55b868977a/OceanDNA-b9722.fa --refList OceanDNA-b9722/target_genomes.txt --output OceanDNA-b9722/fastani_result.tsv --threads 1
[2023-03-16 12:01:45,111] [INFO] Task succeeded: fastANI
[2023-03-16 12:01:45,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:01:45,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:01:45,121] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:01:45,121] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:01:45,122] [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
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	81.3122	463	598	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	77.4864	189	598	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	77.4843	193	598	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.2697	183	598	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.1222	190	598	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.1061	180	598	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.7751	138	598	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.7751	138	598	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.7705	135	598	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	76.6655	124	598	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.5877	102	598	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.3603	92	598	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.3274	85	598	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.1816	83	598	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.1258	101	598	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	75.6324	50	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:01:45,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9722/tc_result.tsv
[2023-03-16 12:01:45,122] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:01:45,122] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:01:45,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/checkm_data
[2023-03-16 12:01:45,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:01:45,126] [INFO] Task started: CheckM
[2023-03-16 12:01:45,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9722/checkm_input OceanDNA-b9722/checkm_result
[2023-03-16 12:02:24,182] [INFO] Task succeeded: CheckM
[2023-03-16 12:02:24,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:02:24,185] [INFO] ===== Completeness check finished =====
[2023-03-16 12:02:24,185] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:02:24,185] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9722/markers.fasta)
[2023-03-16 12:02:24,185] [INFO] Task started: Blastn
[2023-03-16 12:02:24,185] [INFO] Running command: blastn -query OceanDNA-b9722/markers.fasta -db /var/lib/cwl/stg068876ab-dbb4-4f6f-bf91-64c470a06e96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:02:24,978] [INFO] Task succeeded: Blastn
[2023-03-16 12:02:24,979] [INFO] Selected 15 target genomes.
[2023-03-16 12:02:24,979] [INFO] Target genome list was writen to OceanDNA-b9722/target_genomes_gtdb.txt
[2023-03-16 12:02:25,291] [INFO] Task started: fastANI
[2023-03-16 12:02:25,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c839058-820f-4e7c-a0f6-bd55b868977a/OceanDNA-b9722.fa --refList OceanDNA-b9722/target_genomes_gtdb.txt --output OceanDNA-b9722/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:02:36,852] [INFO] Task succeeded: fastANI
[2023-03-16 12:02:36,862] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:02:36,862] [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_003008425.1	s__Aurantibacter aestuarii	81.3121	463	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211855.2	s__Lacinutrix sp000211855	77.4512	201	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.4258	208	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	77.363	198	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_003259525.1	s__Olleya aquimaris	77.2647	181	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.1471	184	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.1222	190	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	77.1061	180	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	77.0191	181	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_002831665.1	s__Lacinutrix sp002831665	76.9729	207	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.7751	138	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.7705	135	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.675	121	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	76.6433	123	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	76.3106	90	598	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:02:36,862] [INFO] GTDB search result was written to OceanDNA-b9722/result_gtdb.tsv
[2023-03-16 12:02:36,863] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:02:36,864] [INFO] DFAST_QC result json was written to OceanDNA-b9722/dqc_result.json
[2023-03-16 12:02:36,865] [INFO] DFAST_QC completed!
[2023-03-16 12:02:36,865] [INFO] Total running time: 0h1m19s