[2023-03-16 15:26:08,217] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference
[2023-03-16 15:26:09,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:09,503] [INFO] Task started: Prodigal
[2023-03-16 15:26:09,503] [INFO] Running command: cat /var/lib/cwl/stg82a03093-8fb7-416f-a3a7-157242c59746/OceanDNA-b39032.fa | prodigal -d OceanDNA-b39032/cds.fna -a OceanDNA-b39032/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:44,800] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:44,800] [INFO] Task started: HMMsearch
[2023-03-16 15:26:44,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b39032/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/reference_markers.hmm OceanDNA-b39032/protein.faa > /dev/null
[2023-03-16 15:26:45,019] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:45,019] [INFO] Found 6/6 markers.
[2023-03-16 15:26:45,042] [INFO] Query marker FASTA was written to OceanDNA-b39032/markers.fasta
[2023-03-16 15:26:45,042] [INFO] Task started: Blastn
[2023-03-16 15:26:45,043] [INFO] Running command: blastn -query OceanDNA-b39032/markers.fasta -db /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/reference_markers.fasta -out OceanDNA-b39032/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:45,794] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:45,795] [INFO] Selected 18 target genomes.
[2023-03-16 15:26:45,795] [INFO] Target genome list was writen to OceanDNA-b39032/target_genomes.txt
[2023-03-16 15:26:45,805] [INFO] Task started: fastANI
[2023-03-16 15:26:45,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a03093-8fb7-416f-a3a7-157242c59746/OceanDNA-b39032.fa --refList OceanDNA-b39032/target_genomes.txt --output OceanDNA-b39032/fastani_result.tsv --threads 1
[2023-03-16 15:26:59,917] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:59,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:59,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:59,928] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 15:26:59,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 15:26:59,928] [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
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	96.6926	1085	1262	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	84.1662	741	1262	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	82.1066	748	1262	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	82.0009	743	1262	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	81.8977	732	1262	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	81.1807	659	1262	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	80.6446	529	1262	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	80.6317	519	1262	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.6085	599	1262	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	80.5958	663	1262	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	80.4966	675	1262	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.3735	593	1262	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	80.318	606	1262	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.1782	528	1262	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.7976	493	1262	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.7864	378	1262	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.5598	553	1262	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7556	453	1262	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:26:59,928] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39032/tc_result.tsv
[2023-03-16 15:26:59,928] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:59,928] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:59,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/checkm_data
[2023-03-16 15:26:59,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:59,934] [INFO] Task started: CheckM
[2023-03-16 15:26:59,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39032/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39032/checkm_input OceanDNA-b39032/checkm_result
[2023-03-16 15:28:13,098] [INFO] Task succeeded: CheckM
[2023-03-16 15:28:13,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:28:13,102] [INFO] ===== Completeness check finished =====
[2023-03-16 15:28:13,102] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:28:13,102] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39032/markers.fasta)
[2023-03-16 15:28:13,103] [INFO] Task started: Blastn
[2023-03-16 15:28:13,104] [INFO] Running command: blastn -query OceanDNA-b39032/markers.fasta -db /var/lib/cwl/stg69bef11f-5f9c-4bf4-b3fe-431623302b04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39032/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:28:14,740] [INFO] Task succeeded: Blastn
[2023-03-16 15:28:14,741] [INFO] Selected 13 target genomes.
[2023-03-16 15:28:14,741] [INFO] Target genome list was writen to OceanDNA-b39032/target_genomes_gtdb.txt
[2023-03-16 15:28:14,880] [INFO] Task started: fastANI
[2023-03-16 15:28:14,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a03093-8fb7-416f-a3a7-157242c59746/OceanDNA-b39032.fa --refList OceanDNA-b39032/target_genomes_gtdb.txt --output OceanDNA-b39032/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:28:31,013] [INFO] Task succeeded: fastANI
[2023-03-16 15:28:31,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 15:28:31,022] [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_000284615.1	s__Marinobacter hydrocarbonoclasticus	96.9218	1115	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	conclusive
GCF_002258215.1	s__Marinobacter vinifirmus	84.1662	741	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_001447155.2	s__Marinobacter sp001447155	82.7924	745	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421165.1	s__Marinobacter daepoensis	81.9931	744	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.99	98.99	0.93	0.93	2	-
GCF_003007715.1	s__Marinobacter shengliensis	81.8928	733	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_003007675.1	s__Marinobacter fuscus	81.1894	658	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114155.1	s__Marinobacter persicus	80.6197	520	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900114925.1	s__Marinobacter pelagius	80.6085	599	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007685.1	s__Marinobacter halophilus	80.5054	674	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650915.1	s__Marinobacter sp001650915	80.3049	604	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_008107725.1	s__Marinobacter sp008107725	79.8128	592	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188315.1	s__Marinobacter sp900188315	79.8038	556	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	79.7986	428	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:28:31,022] [INFO] GTDB search result was written to OceanDNA-b39032/result_gtdb.tsv
[2023-03-16 15:28:31,022] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:28:31,024] [INFO] DFAST_QC result json was written to OceanDNA-b39032/dqc_result.json
[2023-03-16 15:28:31,024] [INFO] DFAST_QC completed!
[2023-03-16 15:28:31,024] [INFO] Total running time: 0h2m23s