[2023-03-17 23:09:44,520] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:09:44,521] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:09:44,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference
[2023-03-17 23:09:45,711] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:09:45,712] [INFO] Task started: Prodigal
[2023-03-17 23:09:45,712] [INFO] Running command: cat /var/lib/cwl/stg2568827d-231e-4f97-8fd4-25757130cc07/OceanDNA-b39159.fa | prodigal -d OceanDNA-b39159/cds.fna -a OceanDNA-b39159/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:10:05,089] [INFO] Task succeeded: Prodigal
[2023-03-17 23:10:05,090] [INFO] Task started: HMMsearch
[2023-03-17 23:10:05,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b39159/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/reference_markers.hmm OceanDNA-b39159/protein.faa > /dev/null
[2023-03-17 23:10:05,312] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:10:05,313] [INFO] Found 6/6 markers.
[2023-03-17 23:10:05,339] [INFO] Query marker FASTA was written to OceanDNA-b39159/markers.fasta
[2023-03-17 23:10:05,340] [INFO] Task started: Blastn
[2023-03-17 23:10:05,340] [INFO] Running command: blastn -query OceanDNA-b39159/markers.fasta -db /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/reference_markers.fasta -out OceanDNA-b39159/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:06,128] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:06,132] [INFO] Selected 16 target genomes.
[2023-03-17 23:10:06,132] [INFO] Target genome list was writen to OceanDNA-b39159/target_genomes.txt
[2023-03-17 23:10:06,138] [INFO] Task started: fastANI
[2023-03-17 23:10:06,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg2568827d-231e-4f97-8fd4-25757130cc07/OceanDNA-b39159.fa --refList OceanDNA-b39159/target_genomes.txt --output OceanDNA-b39159/fastani_result.tsv --threads 1
[2023-03-17 23:10:18,386] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:18,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:10:18,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:10:18,396] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 23:10:18,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 23:10:18,397] [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 vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	96.9349	926	1032	95	conclusive
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	82.8498	702	1032	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	82.8195	706	1032	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	82.6464	689	1032	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	81.4624	624	1032	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	81.3976	612	1032	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	81.1389	617	1032	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	81.1184	541	1032	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	80.7435	585	1032	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.9863	516	1032	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.6448	522	1032	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	79.6338	511	1032	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.6133	505	1032	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.5441	459	1032	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.1172	409	1032	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.9842	444	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:10:18,399] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39159/tc_result.tsv
[2023-03-17 23:10:18,401] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:10:18,401] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:10:18,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/checkm_data
[2023-03-17 23:10:18,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:10:18,408] [INFO] Task started: CheckM
[2023-03-17 23:10:18,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39159/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39159/checkm_input OceanDNA-b39159/checkm_result
[2023-03-17 23:11:07,629] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:07,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:07,694] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:07,695] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:07,695] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39159/markers.fasta)
[2023-03-17 23:11:07,696] [INFO] Task started: Blastn
[2023-03-17 23:11:07,696] [INFO] Running command: blastn -query OceanDNA-b39159/markers.fasta -db /var/lib/cwl/stg0f5954ee-caec-47a8-ba06-77a015cae805/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39159/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:09,064] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:09,069] [INFO] Selected 13 target genomes.
[2023-03-17 23:11:09,069] [INFO] Target genome list was writen to OceanDNA-b39159/target_genomes_gtdb.txt
[2023-03-17 23:11:09,091] [INFO] Task started: fastANI
[2023-03-17 23:11:09,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg2568827d-231e-4f97-8fd4-25757130cc07/OceanDNA-b39159.fa --refList OceanDNA-b39159/target_genomes_gtdb.txt --output OceanDNA-b39159/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:11:18,989] [INFO] Task succeeded: fastANI
[2023-03-17 23:11:18,997] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:11:18,998] [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_002258215.1	s__Marinobacter vinifirmus	96.9519	925	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	conclusive
GCF_001447155.2	s__Marinobacter sp001447155	83.1306	722	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	82.8498	702	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	82.5826	696	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003007685.1	s__Marinobacter halophilus	81.4624	624	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018402255.1	s__Marinobacter sp018402255	81.1723	609	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_900114155.1	s__Marinobacter persicus	81.1044	543	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003315345.1	s__Marinobacter pelagius_A	81.0242	622	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007675.1	s__Marinobacter fuscus	80.7259	587	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	80.7076	522	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	79.92	409	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	79.7763	505	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	79.6076	505	1032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:11:18,999] [INFO] GTDB search result was written to OceanDNA-b39159/result_gtdb.tsv
[2023-03-17 23:11:18,999] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:11:19,002] [INFO] DFAST_QC result json was written to OceanDNA-b39159/dqc_result.json
[2023-03-17 23:11:19,002] [INFO] DFAST_QC completed!
[2023-03-17 23:11:19,002] [INFO] Total running time: 0h1m34s