[2023-03-18 21:43:12,598] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:43:12,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:43:12,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference
[2023-03-18 21:43:13,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:43:13,720] [INFO] Task started: Prodigal
[2023-03-18 21:43:13,720] [INFO] Running command: cat /var/lib/cwl/stgb2d897af-02a9-4b3f-a9be-cab08a249d20/OceanDNA-b36302.fa | prodigal -d OceanDNA-b36302/cds.fna -a OceanDNA-b36302/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:43:25,672] [INFO] Task succeeded: Prodigal
[2023-03-18 21:43:25,673] [INFO] Task started: HMMsearch
[2023-03-18 21:43:25,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b36302/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/reference_markers.hmm OceanDNA-b36302/protein.faa > /dev/null
[2023-03-18 21:43:25,851] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:43:25,852] [INFO] Found 6/6 markers.
[2023-03-18 21:43:25,866] [INFO] Query marker FASTA was written to OceanDNA-b36302/markers.fasta
[2023-03-18 21:43:25,867] [INFO] Task started: Blastn
[2023-03-18 21:43:25,867] [INFO] Running command: blastn -query OceanDNA-b36302/markers.fasta -db /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/reference_markers.fasta -out OceanDNA-b36302/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:43:26,468] [INFO] Task succeeded: Blastn
[2023-03-18 21:43:26,469] [INFO] Selected 25 target genomes.
[2023-03-18 21:43:26,469] [INFO] Target genome list was writen to OceanDNA-b36302/target_genomes.txt
[2023-03-18 21:43:26,480] [INFO] Task started: fastANI
[2023-03-18 21:43:26,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2d897af-02a9-4b3f-a9be-cab08a249d20/OceanDNA-b36302.fa --refList OceanDNA-b36302/target_genomes.txt --output OceanDNA-b36302/fastani_result.tsv --threads 1
[2023-03-18 21:43:40,800] [INFO] Task succeeded: fastANI
[2023-03-18 21:43:40,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:43:40,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:43:40,806] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:43:40,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:43:40,806] [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
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.589	72	728	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.5561	51	728	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.556	67	728	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	75.9131	76	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:43:40,806] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36302/tc_result.tsv
[2023-03-18 21:43:40,806] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:43:40,806] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:43:40,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/checkm_data
[2023-03-18 21:43:40,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:43:40,810] [INFO] Task started: CheckM
[2023-03-18 21:43:40,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36302/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36302/checkm_input OceanDNA-b36302/checkm_result
[2023-03-18 21:44:14,105] [INFO] Task succeeded: CheckM
[2023-03-18 21:44:14,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:44:14,108] [INFO] ===== Completeness check finished =====
[2023-03-18 21:44:14,108] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:44:14,108] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36302/markers.fasta)
[2023-03-18 21:44:14,109] [INFO] Task started: Blastn
[2023-03-18 21:44:14,109] [INFO] Running command: blastn -query OceanDNA-b36302/markers.fasta -db /var/lib/cwl/stg907da36b-2974-4fa6-ba3b-90f519f8ccd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36302/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:44:15,069] [INFO] Task succeeded: Blastn
[2023-03-18 21:44:15,070] [INFO] Selected 13 target genomes.
[2023-03-18 21:44:15,070] [INFO] Target genome list was writen to OceanDNA-b36302/target_genomes_gtdb.txt
[2023-03-18 21:44:15,079] [INFO] Task started: fastANI
[2023-03-18 21:44:15,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2d897af-02a9-4b3f-a9be-cab08a249d20/OceanDNA-b36302.fa --refList OceanDNA-b36302/target_genomes_gtdb.txt --output OceanDNA-b36302/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:44:21,337] [INFO] Task succeeded: fastANI
[2023-03-18 21:44:21,344] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:44:21,344] [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_013215825.1	s__GCA-002733105 sp013215825	99.9683	719	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215775.1	s__GCA-002733105 sp013215775	78.6178	241	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733335.1	s__GCA-002733105 sp002733335	78.506	199	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139345.1	s__GCA-002733105 sp013139345	78.4746	202	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733715.2	s__GCA-002733105 sp002733715	78.39	226	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733505.1	s__GCA-002733105 sp002733505	78.2728	222	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402245.1	s__GCA-002733105 sp002402245	78.0624	213	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	77.6403	157	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053005.1	s__GCA-002733105 sp011053005	77.4459	173	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.319	167	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	76.8246	111	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:44:21,344] [INFO] GTDB search result was written to OceanDNA-b36302/result_gtdb.tsv
[2023-03-18 21:44:21,344] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:44:21,345] [INFO] DFAST_QC result json was written to OceanDNA-b36302/dqc_result.json
[2023-03-18 21:44:21,345] [INFO] DFAST_QC completed!
[2023-03-18 21:44:21,345] [INFO] Total running time: 0h1m9s