[2023-03-17 15:54:38,090] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:54:38,090] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:54:38,090] [INFO] DQC Reference Directory: /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference
[2023-03-17 15:54:39,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:54:39,304] [INFO] Task started: Prodigal
[2023-03-17 15:54:39,304] [INFO] Running command: cat /var/lib/cwl/stg090da669-664b-4424-990a-a53ca61b16e0/OceanDNA-b34119.fa | prodigal -d OceanDNA-b34119/cds.fna -a OceanDNA-b34119/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:54:51,968] [INFO] Task succeeded: Prodigal
[2023-03-17 15:54:51,969] [INFO] Task started: HMMsearch
[2023-03-17 15:54:51,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b34119/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/reference_markers.hmm OceanDNA-b34119/protein.faa > /dev/null
[2023-03-17 15:54:52,132] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:54:52,133] [INFO] Found 6/6 markers.
[2023-03-17 15:54:52,150] [INFO] Query marker FASTA was written to OceanDNA-b34119/markers.fasta
[2023-03-17 15:54:52,150] [INFO] Task started: Blastn
[2023-03-17 15:54:52,150] [INFO] Running command: blastn -query OceanDNA-b34119/markers.fasta -db /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/reference_markers.fasta -out OceanDNA-b34119/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:54:52,680] [INFO] Task succeeded: Blastn
[2023-03-17 15:54:52,681] [INFO] Selected 26 target genomes.
[2023-03-17 15:54:52,681] [INFO] Target genome list was writen to OceanDNA-b34119/target_genomes.txt
[2023-03-17 15:54:52,697] [INFO] Task started: fastANI
[2023-03-17 15:54:52,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg090da669-664b-4424-990a-a53ca61b16e0/OceanDNA-b34119.fa --refList OceanDNA-b34119/target_genomes.txt --output OceanDNA-b34119/fastani_result.tsv --threads 1
[2023-03-17 15:55:04,783] [INFO] Task succeeded: fastANI
[2023-03-17 15:55:04,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:55:04,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:55:04,787] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:55:04,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 15:55:04,787] [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
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	76.8404	58	738	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	76.7771	62	738	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	76.5487	87	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 15:55:04,787] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34119/tc_result.tsv
[2023-03-17 15:55:04,787] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:55:04,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:55:04,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/checkm_data
[2023-03-17 15:55:04,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:55:04,792] [INFO] Task started: CheckM
[2023-03-17 15:55:04,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34119/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34119/checkm_input OceanDNA-b34119/checkm_result
[2023-03-17 15:55:39,585] [INFO] Task succeeded: CheckM
[2023-03-17 15:55:39,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 15:55:39,587] [INFO] ===== Completeness check finished =====
[2023-03-17 15:55:39,587] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:55:39,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34119/markers.fasta)
[2023-03-17 15:55:39,588] [INFO] Task started: Blastn
[2023-03-17 15:55:39,588] [INFO] Running command: blastn -query OceanDNA-b34119/markers.fasta -db /var/lib/cwl/stga2ca7df9-c56d-40ba-bc2b-1a87fa4f71cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34119/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:55:40,331] [INFO] Task succeeded: Blastn
[2023-03-17 15:55:40,332] [INFO] Selected 24 target genomes.
[2023-03-17 15:55:40,332] [INFO] Target genome list was writen to OceanDNA-b34119/target_genomes_gtdb.txt
[2023-03-17 15:55:40,547] [INFO] Task started: fastANI
[2023-03-17 15:55:40,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg090da669-664b-4424-990a-a53ca61b16e0/OceanDNA-b34119.fa --refList OceanDNA-b34119/target_genomes_gtdb.txt --output OceanDNA-b34119/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:55:51,860] [INFO] Task succeeded: fastANI
[2023-03-17 15:55:51,867] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:55:51,867] [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_900143275.1	s__Nitrosomonas cryotolerans	77.4417	136	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016708955.1	s__Nitrosomonas sp016708955	76.9954	85	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455205.1	s__Nitrosomonas ureae	76.7771	62	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.53	97.95	0.91	0.88	6	-
GCF_900108305.1	s__Nitrosomonas ureae_B	76.6599	60	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219585.1	s__Nitrosomonas sp000219585	76.5608	95	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017994575.1	s__Nitrosomonas sp017994575	76.5226	75	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.80	99.80	0.86	0.86	2	-
GCA_016721865.1	s__Nitrosomonas sp016721865	76.3952	85	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175095.2	s__Nitrosomonas sp000175095	76.379	69	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.06	96.06	0.86	0.86	2	-
GCA_902826115.1	s__Nitrosomonas sp902826115	76.2986	86	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.11	98.94	0.89	0.89	3	-
GCF_003268955.1	s__Nitrosomonas sp003268955	76.2556	73	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 15:55:51,867] [INFO] GTDB search result was written to OceanDNA-b34119/result_gtdb.tsv
[2023-03-17 15:55:51,867] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:55:51,868] [INFO] DFAST_QC result json was written to OceanDNA-b34119/dqc_result.json
[2023-03-17 15:55:51,869] [INFO] DFAST_QC completed!
[2023-03-17 15:55:51,869] [INFO] Total running time: 0h1m14s