[2023-03-19 04:29:38,146] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference
[2023-03-19 04:29:39,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,833] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,833] [INFO] Running command: cat /var/lib/cwl/stgc73103c1-8d6b-46ed-8331-abf81527f8ed/OceanDNA-b36208.fa | prodigal -d OceanDNA-b36208/cds.fna -a OceanDNA-b36208/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:48,879] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:48,879] [INFO] Task started: HMMsearch
[2023-03-19 04:29:48,879] [INFO] Running command: hmmsearch --tblout OceanDNA-b36208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/reference_markers.hmm OceanDNA-b36208/protein.faa > /dev/null
[2023-03-19 04:29:49,070] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:49,071] [INFO] Found 6/6 markers.
[2023-03-19 04:29:49,082] [INFO] Query marker FASTA was written to OceanDNA-b36208/markers.fasta
[2023-03-19 04:29:49,082] [INFO] Task started: Blastn
[2023-03-19 04:29:49,082] [INFO] Running command: blastn -query OceanDNA-b36208/markers.fasta -db /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/reference_markers.fasta -out OceanDNA-b36208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:49,668] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:49,669] [INFO] Selected 27 target genomes.
[2023-03-19 04:29:49,670] [INFO] Target genome list was writen to OceanDNA-b36208/target_genomes.txt
[2023-03-19 04:29:49,683] [INFO] Task started: fastANI
[2023-03-19 04:29:49,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgc73103c1-8d6b-46ed-8331-abf81527f8ed/OceanDNA-b36208.fa --refList OceanDNA-b36208/target_genomes.txt --output OceanDNA-b36208/fastani_result.tsv --threads 1
[2023-03-19 04:30:03,731] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:03,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:03,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:03,736] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:03,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:03,736] [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	77.1974	72	542	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.6963	67	542	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	76.5538	58	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:03,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36208/tc_result.tsv
[2023-03-19 04:30:03,737] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:03,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:03,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/checkm_data
[2023-03-19 04:30:03,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:03,741] [INFO] Task started: CheckM
[2023-03-19 04:30:03,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36208/checkm_input OceanDNA-b36208/checkm_result
[2023-03-19 04:30:30,939] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:30,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:30,942] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:30,942] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:30,942] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36208/markers.fasta)
[2023-03-19 04:30:30,942] [INFO] Task started: Blastn
[2023-03-19 04:30:30,942] [INFO] Running command: blastn -query OceanDNA-b36208/markers.fasta -db /var/lib/cwl/stg2eed0339-39ee-4cba-bfdf-acee3d1ec411/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:31,903] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:31,904] [INFO] Selected 16 target genomes.
[2023-03-19 04:30:31,904] [INFO] Target genome list was writen to OceanDNA-b36208/target_genomes_gtdb.txt
[2023-03-19 04:30:31,942] [INFO] Task started: fastANI
[2023-03-19 04:30:31,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgc73103c1-8d6b-46ed-8331-abf81527f8ed/OceanDNA-b36208.fa --refList OceanDNA-b36208/target_genomes_gtdb.txt --output OceanDNA-b36208/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:37,798] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:37,808] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:37,808] [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_905479985.1	s__GCA-002733105 sp905479985	79.2811	291	542	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_018646825.1	s__GCA-002733105 sp018646825	79.1248	243	542	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	78.1313	142	542	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	77.3788	90	542	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_905181885.1	s__GCA-002733105 sp905181885	77.352	112	542	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	77.2356	96	542	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	77.1437	79	542	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_014859375.1	s__GCA-002733105 sp014859375	77.0614	103	542	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_003645385.1	s__GCA-002733105 sp003645385	76.8623	72	542	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_002733335.1	s__GCA-002733105 sp002733335	76.8339	72	542	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	76.769	76	542	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	76.7545	83	542	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	76.6469	73	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156355.1	s__Methylophaga thiooxydans	76.5569	59	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	96.48	96.37	0.89	0.88	3	-
GCA_013139345.1	s__GCA-002733105 sp013139345	76.4777	68	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:37,808] [INFO] GTDB search result was written to OceanDNA-b36208/result_gtdb.tsv
[2023-03-19 04:30:37,808] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:37,809] [INFO] DFAST_QC result json was written to OceanDNA-b36208/dqc_result.json
[2023-03-19 04:30:37,810] [INFO] DFAST_QC completed!
[2023-03-19 04:30:37,810] [INFO] Total running time: 0h0m60s