[2023-03-18 20:55:47,252] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,252] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stg99963197-999d-4596-8338-97292a34011c/OceanDNA-b36291.fa | prodigal -d OceanDNA-b36291/cds.fna -a OceanDNA-b36291/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:56:04,877] [INFO] Task succeeded: Prodigal
[2023-03-18 20:56:04,877] [INFO] Task started: HMMsearch
[2023-03-18 20:56:04,877] [INFO] Running command: hmmsearch --tblout OceanDNA-b36291/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/reference_markers.hmm OceanDNA-b36291/protein.faa > /dev/null
[2023-03-18 20:56:05,069] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:56:05,069] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg99963197-999d-4596-8338-97292a34011c/OceanDNA-b36291.fa]
[2023-03-18 20:56:05,087] [INFO] Query marker FASTA was written to OceanDNA-b36291/markers.fasta
[2023-03-18 20:56:05,088] [INFO] Task started: Blastn
[2023-03-18 20:56:05,088] [INFO] Running command: blastn -query OceanDNA-b36291/markers.fasta -db /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/reference_markers.fasta -out OceanDNA-b36291/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:05,653] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:05,653] [INFO] Selected 25 target genomes.
[2023-03-18 20:56:05,654] [INFO] Target genome list was writen to OceanDNA-b36291/target_genomes.txt
[2023-03-18 20:56:05,668] [INFO] Task started: fastANI
[2023-03-18 20:56:05,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg99963197-999d-4596-8338-97292a34011c/OceanDNA-b36291.fa --refList OceanDNA-b36291/target_genomes.txt --output OceanDNA-b36291/fastani_result.tsv --threads 1
[2023-03-18 20:56:17,976] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:17,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:17,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:17,981] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:17,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:56:17,981] [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 thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	76.5205	89	1007	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.5115	72	1007	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.5067	99	1007	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.3983	75	1007	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.3607	94	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:56:17,982] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36291/tc_result.tsv
[2023-03-18 20:56:17,982] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:17,982] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:17,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/checkm_data
[2023-03-18 20:56:17,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:17,987] [INFO] Task started: CheckM
[2023-03-18 20:56:17,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36291/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36291/checkm_input OceanDNA-b36291/checkm_result
[2023-03-18 20:57:00,967] [INFO] Task succeeded: CheckM
[2023-03-18 20:57:00,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:57:00,969] [INFO] ===== Completeness check finished =====
[2023-03-18 20:57:00,969] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:57:00,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36291/markers.fasta)
[2023-03-18 20:57:00,970] [INFO] Task started: Blastn
[2023-03-18 20:57:00,970] [INFO] Running command: blastn -query OceanDNA-b36291/markers.fasta -db /var/lib/cwl/stg49a2c53f-f351-4ab7-a7a5-48e163039a1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36291/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:57:01,837] [INFO] Task succeeded: Blastn
[2023-03-18 20:57:01,838] [INFO] Selected 14 target genomes.
[2023-03-18 20:57:01,838] [INFO] Target genome list was writen to OceanDNA-b36291/target_genomes_gtdb.txt
[2023-03-18 20:57:01,982] [INFO] Task started: fastANI
[2023-03-18 20:57:01,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg99963197-999d-4596-8338-97292a34011c/OceanDNA-b36291.fa --refList OceanDNA-b36291/target_genomes_gtdb.txt --output OceanDNA-b36291/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:57:07,742] [INFO] Task succeeded: fastANI
[2023-03-18 20:57:07,750] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:57:07,751] [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_011053005.1	s__GCA-002733105 sp011053005	81.7809	575	1007	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	77.7793	150	1007	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	77.5324	169	1007	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_013215775.1	s__GCA-002733105 sp013215775	77.4836	185	1007	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	77.463	165	1007	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_013215825.1	s__GCA-002733105 sp013215825	77.439	200	1007	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	77.4336	180	1007	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	77.3646	149	1007	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_905479985.1	s__GCA-002733105 sp905479985	77.2372	112	1007	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_002163085.1	s__41-12-T18 sp002163085	77.2209	149	1007	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_002400805.1	s__41-12-T18 sp002400805	77.1727	73	1007	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_002163115.1	s__41-12-T18 sp002163115	77.1435	149	1007	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_003645385.1	s__GCA-002733105 sp003645385	77.1028	131	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	98.88	98.88	0.61	0.61	2	-
GCA_002733105.1	s__GCA-002733105 sp002733105	76.9696	150	1007	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 20:57:07,751] [INFO] GTDB search result was written to OceanDNA-b36291/result_gtdb.tsv
[2023-03-18 20:57:07,751] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:57:07,752] [INFO] DFAST_QC result json was written to OceanDNA-b36291/dqc_result.json
[2023-03-18 20:57:07,752] [INFO] DFAST_QC completed!
[2023-03-18 20:57:07,752] [INFO] Total running time: 0h1m21s