[2023-03-15 11:09:10,835] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,835] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference
[2023-03-15 11:09:12,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,075] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,075] [INFO] Running command: cat /var/lib/cwl/stgd97b9a0e-a334-4acd-929d-47ec649be93e/OceanDNA-b36289.fa | prodigal -d OceanDNA-b36289/cds.fna -a OceanDNA-b36289/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:26,206] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:26,206] [INFO] Task started: HMMsearch
[2023-03-15 11:09:26,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b36289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/reference_markers.hmm OceanDNA-b36289/protein.faa > /dev/null
[2023-03-15 11:09:26,445] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:26,445] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd97b9a0e-a334-4acd-929d-47ec649be93e/OceanDNA-b36289.fa]
[2023-03-15 11:09:26,461] [INFO] Query marker FASTA was written to OceanDNA-b36289/markers.fasta
[2023-03-15 11:09:26,461] [INFO] Task started: Blastn
[2023-03-15 11:09:26,462] [INFO] Running command: blastn -query OceanDNA-b36289/markers.fasta -db /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/reference_markers.fasta -out OceanDNA-b36289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:27,237] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:27,432] [INFO] Selected 22 target genomes.
[2023-03-15 11:09:27,432] [INFO] Target genome list was writen to OceanDNA-b36289/target_genomes.txt
[2023-03-15 11:09:27,443] [INFO] Task started: fastANI
[2023-03-15 11:09:27,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgd97b9a0e-a334-4acd-929d-47ec649be93e/OceanDNA-b36289.fa --refList OceanDNA-b36289/target_genomes.txt --output OceanDNA-b36289/fastani_result.tsv --threads 1
[2023-03-15 11:09:42,195] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:42,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:42,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:42,201] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:42,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:42,201] [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	76.6418	95	851	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.4602	100	851	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.4312	92	851	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.4123	61	851	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.2198	79	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:42,202] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36289/tc_result.tsv
[2023-03-15 11:09:42,202] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:42,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:42,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/checkm_data
[2023-03-15 11:09:42,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:42,207] [INFO] Task started: CheckM
[2023-03-15 11:09:42,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36289/checkm_input OceanDNA-b36289/checkm_result
[2023-03-15 11:10:20,543] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:20,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:20,546] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:20,546] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:20,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36289/markers.fasta)
[2023-03-15 11:10:20,546] [INFO] Task started: Blastn
[2023-03-15 11:10:20,546] [INFO] Running command: blastn -query OceanDNA-b36289/markers.fasta -db /var/lib/cwl/stg404662ae-1d7f-468e-b6a0-891ccc6c628d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:21,488] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:21,489] [INFO] Selected 12 target genomes.
[2023-03-15 11:10:21,489] [INFO] Target genome list was writen to OceanDNA-b36289/target_genomes_gtdb.txt
[2023-03-15 11:10:21,499] [INFO] Task started: fastANI
[2023-03-15 11:10:21,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgd97b9a0e-a334-4acd-929d-47ec649be93e/OceanDNA-b36289.fa --refList OceanDNA-b36289/target_genomes_gtdb.txt --output OceanDNA-b36289/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:26,458] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:26,466] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:26,466] [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	82.6018	567	851	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	77.549	164	851	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	77.3545	166	851	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	77.3492	160	851	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_013215775.1	s__GCA-002733105 sp013215775	77.2558	158	851	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	77.2269	201	851	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	77.1967	151	851	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	77.1145	136	851	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_013139345.1	s__GCA-002733105 sp013139345	76.9808	140	851	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	76.9782	140	851	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_002363955.1	s__Methylophaga sp002363955	76.4761	67	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	-
GCA_905181885.1	s__GCA-002733105 sp905181885	76.3659	72	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:26,466] [INFO] GTDB search result was written to OceanDNA-b36289/result_gtdb.tsv
[2023-03-15 11:10:26,466] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:26,467] [INFO] DFAST_QC result json was written to OceanDNA-b36289/dqc_result.json
[2023-03-15 11:10:26,467] [INFO] DFAST_QC completed!
[2023-03-15 11:10:26,468] [INFO] Total running time: 0h1m16s