[2023-03-19 00:44:19,973] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference
[2023-03-19 00:44:21,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,064] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,064] [INFO] Running command: cat /var/lib/cwl/stg844e4bd5-c638-4b87-84c0-8c377051d88a/OceanDNA-b23546.fa | prodigal -d OceanDNA-b23546/cds.fna -a OceanDNA-b23546/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:41,579] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:41,579] [INFO] Task started: HMMsearch
[2023-03-19 00:44:41,580] [INFO] Running command: hmmsearch --tblout OceanDNA-b23546/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/reference_markers.hmm OceanDNA-b23546/protein.faa > /dev/null
[2023-03-19 00:44:41,770] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:41,771] [INFO] Found 6/6 markers.
[2023-03-19 00:44:41,792] [INFO] Query marker FASTA was written to OceanDNA-b23546/markers.fasta
[2023-03-19 00:44:41,794] [INFO] Task started: Blastn
[2023-03-19 00:44:41,794] [INFO] Running command: blastn -query OceanDNA-b23546/markers.fasta -db /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/reference_markers.fasta -out OceanDNA-b23546/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:42,490] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:42,491] [INFO] Selected 31 target genomes.
[2023-03-19 00:44:42,491] [INFO] Target genome list was writen to OceanDNA-b23546/target_genomes.txt
[2023-03-19 00:44:42,511] [INFO] Task started: fastANI
[2023-03-19 00:44:42,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg844e4bd5-c638-4b87-84c0-8c377051d88a/OceanDNA-b23546.fa --refList OceanDNA-b23546/target_genomes.txt --output OceanDNA-b23546/fastani_result.tsv --threads 1
[2023-03-19 00:45:00,743] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:00,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:45:00,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:45:00,749] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:45:00,749] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:45:00,749] [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
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.5099	70	1076	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.1252	58	1076	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.0479	76	1076	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	76.0	62	1076	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	75.9852	69	1076	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	75.9808	65	1076	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	75.9387	85	1076	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:45:00,750] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23546/tc_result.tsv
[2023-03-19 00:45:00,750] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:45:00,750] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:45:00,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/checkm_data
[2023-03-19 00:45:00,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:45:00,766] [INFO] Task started: CheckM
[2023-03-19 00:45:00,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23546/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23546/checkm_input OceanDNA-b23546/checkm_result
[2023-03-19 00:45:53,720] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:53,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:53,724] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:53,724] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:53,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23546/markers.fasta)
[2023-03-19 00:45:53,725] [INFO] Task started: Blastn
[2023-03-19 00:45:53,725] [INFO] Running command: blastn -query OceanDNA-b23546/markers.fasta -db /var/lib/cwl/stg195d0bd4-5655-4838-be76-e2394faec25e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23546/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:54,970] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:54,971] [INFO] Selected 29 target genomes.
[2023-03-19 00:45:54,971] [INFO] Target genome list was writen to OceanDNA-b23546/target_genomes_gtdb.txt
[2023-03-19 00:45:55,026] [INFO] Task started: fastANI
[2023-03-19 00:45:55,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg844e4bd5-c638-4b87-84c0-8c377051d88a/OceanDNA-b23546.fa --refList OceanDNA-b23546/target_genomes_gtdb.txt --output OceanDNA-b23546/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:46:12,257] [INFO] Task succeeded: fastANI
[2023-03-19 00:46:12,264] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:46:12,264] [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_002709235.1	s__Hirschia sp002709235	99.9566	1052	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hirschia	95.0	99.96	99.93	0.96	0.95	3	conclusive
GCF_003576285.1	s__Henriciella sp003576285	76.2552	72	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_005871165.1	s__Maricaulis sp005871165	76.2344	53	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	76.1252	58	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483135.1	s__UBA7672 sp002483135	76.1097	66	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682755.1	s__Hyphomonas beringensis	76.0	62	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685235.1	s__Hyphomonas adhaerens	75.9852	69	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000682715.1	s__Hyphomonas atlantica	75.9808	65	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_016714495.1	s__UBA7672 sp016714495	75.9554	61	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125405.1	s__UBA7672 sp016125405	75.8799	58	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	75.5061	53	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:46:12,264] [INFO] GTDB search result was written to OceanDNA-b23546/result_gtdb.tsv
[2023-03-19 00:46:12,264] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:46:12,266] [INFO] DFAST_QC result json was written to OceanDNA-b23546/dqc_result.json
[2023-03-19 00:46:12,266] [INFO] DFAST_QC completed!
[2023-03-19 00:46:12,266] [INFO] Total running time: 0h1m52s