[2023-03-14 11:13:58,992] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,992] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference
[2023-03-14 11:14:00,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stga559d86c-ec13-40c0-a839-e2a821724930/OceanDNA-b36398.fa | prodigal -d OceanDNA-b36398/cds.fna -a OceanDNA-b36398/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:17,654] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:17,654] [INFO] Task started: HMMsearch
[2023-03-14 11:14:17,654] [INFO] Running command: hmmsearch --tblout OceanDNA-b36398/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/reference_markers.hmm OceanDNA-b36398/protein.faa > /dev/null
[2023-03-14 11:14:17,868] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:17,869] [INFO] Found 6/6 markers.
[2023-03-14 11:14:17,887] [INFO] Query marker FASTA was written to OceanDNA-b36398/markers.fasta
[2023-03-14 11:14:17,887] [INFO] Task started: Blastn
[2023-03-14 11:14:17,887] [INFO] Running command: blastn -query OceanDNA-b36398/markers.fasta -db /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/reference_markers.fasta -out OceanDNA-b36398/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:18,487] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:18,488] [INFO] Selected 20 target genomes.
[2023-03-14 11:14:18,488] [INFO] Target genome list was writen to OceanDNA-b36398/target_genomes.txt
[2023-03-14 11:14:18,503] [INFO] Task started: fastANI
[2023-03-14 11:14:18,503] [INFO] Running command: fastANI --query /var/lib/cwl/stga559d86c-ec13-40c0-a839-e2a821724930/OceanDNA-b36398.fa --refList OceanDNA-b36398/target_genomes.txt --output OceanDNA-b36398/fastani_result.tsv --threads 1
[2023-03-14 11:14:30,108] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:30,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:30,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:30,115] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:30,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:30,115] [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	84.4047	726	1002	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	83.8343	759	1002	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	78.1562	221	1002	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	77.4837	112	1002	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.9898	109	1002	95	below_threshold
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	76.7672	93	1002	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:30,115] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36398/tc_result.tsv
[2023-03-14 11:14:30,115] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:30,116] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:30,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/checkm_data
[2023-03-14 11:14:30,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:30,121] [INFO] Task started: CheckM
[2023-03-14 11:14:30,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36398/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36398/checkm_input OceanDNA-b36398/checkm_result
[2023-03-14 11:15:15,217] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:15,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:15,220] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:15,220] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:15,220] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36398/markers.fasta)
[2023-03-14 11:15:15,222] [INFO] Task started: Blastn
[2023-03-14 11:15:15,222] [INFO] Running command: blastn -query OceanDNA-b36398/markers.fasta -db /var/lib/cwl/stg5bce19b7-ccb4-4e56-b9ac-9d87bd656a38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36398/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:16,195] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:16,196] [INFO] Selected 13 target genomes.
[2023-03-14 11:15:16,196] [INFO] Target genome list was writen to OceanDNA-b36398/target_genomes_gtdb.txt
[2023-03-14 11:15:16,211] [INFO] Task started: fastANI
[2023-03-14 11:15:16,211] [INFO] Running command: fastANI --query /var/lib/cwl/stga559d86c-ec13-40c0-a839-e2a821724930/OceanDNA-b36398.fa --refList OceanDNA-b36398/target_genomes_gtdb.txt --output OceanDNA-b36398/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:23,607] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:23,612] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:15:23,613] [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_002706095.1	s__Methylophaga sp002706095	97.4771	926	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	conclusive
GCF_900114205.1	s__Methylophaga sulfidovorans	84.4028	726	1002	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	83.8096	761	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
GCA_011052985.1	s__Methylophaga aminisulfidivorans_A	79.3182	223	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156355.1	s__Methylophaga thiooxydans	78.1391	222	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_009711715.1	s__Methylophaga sp009711715	77.6101	165	1002	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	77.2929	126	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCA_002354555.1	s__Methylophaga sp002354555	76.9451	118	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.87	98.17	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:23,613] [INFO] GTDB search result was written to OceanDNA-b36398/result_gtdb.tsv
[2023-03-14 11:15:23,613] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:23,614] [INFO] DFAST_QC result json was written to OceanDNA-b36398/dqc_result.json
[2023-03-14 11:15:23,614] [INFO] DFAST_QC completed!
[2023-03-14 11:15:23,614] [INFO] Total running time: 0h1m25s