[2023-03-18 01:11:39,142] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:11:39,142] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:11:39,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference
[2023-03-18 01:11:40,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:11:40,239] [INFO] Task started: Prodigal
[2023-03-18 01:11:40,239] [INFO] Running command: cat /var/lib/cwl/stga8188d51-01dd-44e9-b297-341c979ba78b/OceanDNA-b38971.fa | prodigal -d OceanDNA-b38971/cds.fna -a OceanDNA-b38971/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:12:05,070] [INFO] Task succeeded: Prodigal
[2023-03-18 01:12:05,070] [INFO] Task started: HMMsearch
[2023-03-18 01:12:05,070] [INFO] Running command: hmmsearch --tblout OceanDNA-b38971/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/reference_markers.hmm OceanDNA-b38971/protein.faa > /dev/null
[2023-03-18 01:12:05,313] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:12:05,314] [INFO] Found 6/6 markers.
[2023-03-18 01:12:05,340] [INFO] Query marker FASTA was written to OceanDNA-b38971/markers.fasta
[2023-03-18 01:12:05,341] [INFO] Task started: Blastn
[2023-03-18 01:12:05,341] [INFO] Running command: blastn -query OceanDNA-b38971/markers.fasta -db /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/reference_markers.fasta -out OceanDNA-b38971/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:12:06,133] [INFO] Task succeeded: Blastn
[2023-03-18 01:12:06,135] [INFO] Selected 17 target genomes.
[2023-03-18 01:12:06,135] [INFO] Target genome list was writen to OceanDNA-b38971/target_genomes.txt
[2023-03-18 01:12:06,148] [INFO] Task started: fastANI
[2023-03-18 01:12:06,148] [INFO] Running command: fastANI --query /var/lib/cwl/stga8188d51-01dd-44e9-b297-341c979ba78b/OceanDNA-b38971.fa --refList OceanDNA-b38971/target_genomes.txt --output OceanDNA-b38971/fastani_result.tsv --threads 1
[2023-03-18 01:12:19,574] [INFO] Task succeeded: fastANI
[2023-03-18 01:12:19,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:12:19,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:12:19,594] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 01:12:19,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:12:19,594] [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 alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	98.7304	1230	1331	95	conclusive
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	89.8294	1078	1331	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	89.4627	1013	1331	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	81.064	796	1331	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.0684	627	1331	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	79.9977	650	1331	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.9858	594	1331	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	79.9774	652	1331	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	79.8763	651	1331	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.8515	642	1331	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.7806	539	1331	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	79.4021	519	1331	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.3517	539	1331	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.3486	533	1331	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.2291	416	1331	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.1784	510	1331	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.5497	454	1331	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:12:19,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38971/tc_result.tsv
[2023-03-18 01:12:19,594] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:12:19,594] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:12:19,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/checkm_data
[2023-03-18 01:12:19,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:12:19,601] [INFO] Task started: CheckM
[2023-03-18 01:12:19,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38971/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38971/checkm_input OceanDNA-b38971/checkm_result
[2023-03-18 01:13:21,227] [INFO] Task succeeded: CheckM
[2023-03-18 01:13:21,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:13:21,231] [INFO] ===== Completeness check finished =====
[2023-03-18 01:13:21,231] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:13:21,231] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38971/markers.fasta)
[2023-03-18 01:13:21,232] [INFO] Task started: Blastn
[2023-03-18 01:13:21,232] [INFO] Running command: blastn -query OceanDNA-b38971/markers.fasta -db /var/lib/cwl/stg12fa4031-7f19-4a9a-8668-85511697038a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38971/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:13:22,691] [INFO] Task succeeded: Blastn
[2023-03-18 01:13:22,692] [INFO] Selected 20 target genomes.
[2023-03-18 01:13:22,692] [INFO] Target genome list was writen to OceanDNA-b38971/target_genomes_gtdb.txt
[2023-03-18 01:13:22,705] [INFO] Task started: fastANI
[2023-03-18 01:13:22,705] [INFO] Running command: fastANI --query /var/lib/cwl/stga8188d51-01dd-44e9-b297-341c979ba78b/OceanDNA-b38971.fa --refList OceanDNA-b38971/target_genomes_gtdb.txt --output OceanDNA-b38971/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:13:39,463] [INFO] Task succeeded: fastANI
[2023-03-18 01:13:39,474] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:13:39,474] [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_005871205.1	s__Marinobacter alexandrii	98.7304	1230	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	conclusive
GCA_000830985.1	s__Marinobacter similis	89.8294	1078	1331	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	89.4627	1013	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.173	582	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	80.1264	401	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	80.0791	669	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	80.07	632	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_002933295.1	s__Marinobacter flavimaris	80.0598	628	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_001045555.1	s__Marinobacter subterrani	80.0143	648	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_001650915.1	s__Marinobacter sp001650915	79.9986	691	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_900114925.1	s__Marinobacter pelagius	79.993	594	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	79.9834	648	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCA_018623515.1	s__Marinobacter sp018623515	79.9336	502	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	79.88	572	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	79.8763	651	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.843	643	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.7654	541	1331	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	79.5352	534	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000397065.2	s__Marinobacter lipolyticus	79.4065	519	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	79.3407	532	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:13:39,475] [INFO] GTDB search result was written to OceanDNA-b38971/result_gtdb.tsv
[2023-03-18 01:13:39,475] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:13:39,477] [INFO] DFAST_QC result json was written to OceanDNA-b38971/dqc_result.json
[2023-03-18 01:13:39,477] [INFO] DFAST_QC completed!
[2023-03-18 01:13:39,477] [INFO] Total running time: 0h2m0s