[2023-03-18 22:48:22,582] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:48:22,582] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:48:22,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference
[2023-03-18 22:48:23,662] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:48:23,663] [INFO] Task started: Prodigal
[2023-03-18 22:48:23,663] [INFO] Running command: cat /var/lib/cwl/stg411b5a30-dab7-4815-8ab5-7e06d992b1d4/OceanDNA-b36306.fa | prodigal -d OceanDNA-b36306/cds.fna -a OceanDNA-b36306/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:48:33,722] [INFO] Task succeeded: Prodigal
[2023-03-18 22:48:33,722] [INFO] Task started: HMMsearch
[2023-03-18 22:48:33,722] [INFO] Running command: hmmsearch --tblout OceanDNA-b36306/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/reference_markers.hmm OceanDNA-b36306/protein.faa > /dev/null
[2023-03-18 22:48:33,905] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:48:33,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg411b5a30-dab7-4815-8ab5-7e06d992b1d4/OceanDNA-b36306.fa]
[2023-03-18 22:48:33,922] [INFO] Query marker FASTA was written to OceanDNA-b36306/markers.fasta
[2023-03-18 22:48:33,923] [INFO] Task started: Blastn
[2023-03-18 22:48:33,923] [INFO] Running command: blastn -query OceanDNA-b36306/markers.fasta -db /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/reference_markers.fasta -out OceanDNA-b36306/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:48:34,626] [INFO] Task succeeded: Blastn
[2023-03-18 22:48:34,627] [INFO] Selected 21 target genomes.
[2023-03-18 22:48:34,627] [INFO] Target genome list was writen to OceanDNA-b36306/target_genomes.txt
[2023-03-18 22:48:34,644] [INFO] Task started: fastANI
[2023-03-18 22:48:34,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg411b5a30-dab7-4815-8ab5-7e06d992b1d4/OceanDNA-b36306.fa --refList OceanDNA-b36306/target_genomes.txt --output OceanDNA-b36306/fastani_result.tsv --threads 1
[2023-03-18 22:48:46,076] [INFO] Task succeeded: fastANI
[2023-03-18 22:48:46,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:48:46,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:48:46,082] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:48:46,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:48:46,082] [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	81.9056	391	577	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	78.0983	164	577	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	77.9073	174	577	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.877	97	577	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.7477	98	577	95	below_threshold
Methylophaga frappieri	strain=JAM7	GCA_000260965.1	754477	754477	type	True	76.6365	65	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:48:46,082] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36306/tc_result.tsv
[2023-03-18 22:48:46,083] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:48:46,083] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:48:46,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/checkm_data
[2023-03-18 22:48:46,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:48:46,087] [INFO] Task started: CheckM
[2023-03-18 22:48:46,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36306/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36306/checkm_input OceanDNA-b36306/checkm_result
[2023-03-18 22:49:16,564] [INFO] Task succeeded: CheckM
[2023-03-18 22:49:16,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:49:16,566] [INFO] ===== Completeness check finished =====
[2023-03-18 22:49:16,567] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:49:16,567] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36306/markers.fasta)
[2023-03-18 22:49:16,569] [INFO] Task started: Blastn
[2023-03-18 22:49:16,569] [INFO] Running command: blastn -query OceanDNA-b36306/markers.fasta -db /var/lib/cwl/stg1e6111b3-35bd-40ff-8f46-ec24f52d8c6e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36306/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:49:17,635] [INFO] Task succeeded: Blastn
[2023-03-18 22:49:17,635] [INFO] Selected 18 target genomes.
[2023-03-18 22:49:17,635] [INFO] Target genome list was writen to OceanDNA-b36306/target_genomes_gtdb.txt
[2023-03-18 22:49:17,651] [INFO] Task started: fastANI
[2023-03-18 22:49:17,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg411b5a30-dab7-4815-8ab5-7e06d992b1d4/OceanDNA-b36306.fa --refList OceanDNA-b36306/target_genomes_gtdb.txt --output OceanDNA-b36306/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:49:26,444] [INFO] Task succeeded: fastANI
[2023-03-18 22:49:26,451] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:49:26,451] [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_000156355.1	s__Methylophaga thiooxydans	81.8894	391	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	78.9474	95	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711715.1	s__Methylophaga sp009711715	78.2035	238	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114205.1	s__Methylophaga sulfidovorans	78.0776	165	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706095.1	s__Methylophaga sp002706095	78.006	155	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	-
GCA_014762585.1	s__Methylophaga sp014762585	77.9142	197	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214595.1	s__Methylophaga aminisulfidivorans	77.9073	174	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
GCF_000349205.1	s__Methylophaga lonarensis	76.994	67	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696735.1	s__Methylophaga sp002696735	76.9042	109	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCF_001720165.1	s__Methylophaga muralis	76.7027	94	577	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.83	97.83	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:49:26,451] [INFO] GTDB search result was written to OceanDNA-b36306/result_gtdb.tsv
[2023-03-18 22:49:26,452] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:49:26,453] [INFO] DFAST_QC result json was written to OceanDNA-b36306/dqc_result.json
[2023-03-18 22:49:26,453] [INFO] DFAST_QC completed!
[2023-03-18 22:49:26,453] [INFO] Total running time: 0h1m4s