[2023-03-18 23:14:12,701] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:14:12,701] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:14:12,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference
[2023-03-18 23:14:13,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:14:13,799] [INFO] Task started: Prodigal
[2023-03-18 23:14:13,799] [INFO] Running command: cat /var/lib/cwl/stg418a7b56-d0b1-4b27-94b0-faa3c468e18f/OceanDNA-b36275.fa | prodigal -d OceanDNA-b36275/cds.fna -a OceanDNA-b36275/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:14:23,217] [INFO] Task succeeded: Prodigal
[2023-03-18 23:14:23,217] [INFO] Task started: HMMsearch
[2023-03-18 23:14:23,217] [INFO] Running command: hmmsearch --tblout OceanDNA-b36275/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/reference_markers.hmm OceanDNA-b36275/protein.faa > /dev/null
[2023-03-18 23:14:23,405] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:14:23,405] [INFO] Found 6/6 markers.
[2023-03-18 23:14:23,418] [INFO] Query marker FASTA was written to OceanDNA-b36275/markers.fasta
[2023-03-18 23:14:23,419] [INFO] Task started: Blastn
[2023-03-18 23:14:23,419] [INFO] Running command: blastn -query OceanDNA-b36275/markers.fasta -db /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/reference_markers.fasta -out OceanDNA-b36275/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:14:23,994] [INFO] Task succeeded: Blastn
[2023-03-18 23:14:23,995] [INFO] Selected 26 target genomes.
[2023-03-18 23:14:23,995] [INFO] Target genome list was writen to OceanDNA-b36275/target_genomes.txt
[2023-03-18 23:14:24,011] [INFO] Task started: fastANI
[2023-03-18 23:14:24,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg418a7b56-d0b1-4b27-94b0-faa3c468e18f/OceanDNA-b36275.fa --refList OceanDNA-b36275/target_genomes.txt --output OceanDNA-b36275/fastani_result.tsv --threads 1
[2023-03-18 23:14:37,794] [INFO] Task succeeded: fastANI
[2023-03-18 23:14:37,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:14:37,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:14:37,798] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:14:37,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:14:37,798] [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 aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.4161	50	563	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.1836	63	563	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:14:37,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36275/tc_result.tsv
[2023-03-18 23:14:37,798] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:14:37,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:14:37,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/checkm_data
[2023-03-18 23:14:37,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:14:37,802] [INFO] Task started: CheckM
[2023-03-18 23:14:37,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36275/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36275/checkm_input OceanDNA-b36275/checkm_result
[2023-03-18 23:15:06,029] [INFO] Task succeeded: CheckM
[2023-03-18 23:15:06,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:15:06,032] [INFO] ===== Completeness check finished =====
[2023-03-18 23:15:06,032] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:15:06,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36275/markers.fasta)
[2023-03-18 23:15:06,033] [INFO] Task started: Blastn
[2023-03-18 23:15:06,033] [INFO] Running command: blastn -query OceanDNA-b36275/markers.fasta -db /var/lib/cwl/stg8c96d5f9-583b-4b7e-a040-4ac41882cd39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36275/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:15:06,982] [INFO] Task succeeded: Blastn
[2023-03-18 23:15:06,982] [INFO] Selected 15 target genomes.
[2023-03-18 23:15:06,983] [INFO] Target genome list was writen to OceanDNA-b36275/target_genomes_gtdb.txt
[2023-03-18 23:15:06,996] [INFO] Task started: fastANI
[2023-03-18 23:15:06,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg418a7b56-d0b1-4b27-94b0-faa3c468e18f/OceanDNA-b36275.fa --refList OceanDNA-b36275/target_genomes_gtdb.txt --output OceanDNA-b36275/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:15:13,073] [INFO] Task succeeded: fastANI
[2023-03-18 23:15:13,081] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:15:13,081] [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	96.5457	515	563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018646825.1	s__GCA-002733105 sp018646825	81.5095	331	563	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	77.7619	139	563	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_905181885.1	s__GCA-002733105 sp905181885	77.3951	132	563	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	77.0077	95	563	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	76.9966	113	563	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	76.8421	87	563	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	76.7586	72	563	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_011053005.1	s__GCA-002733105 sp011053005	76.6281	101	563	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	76.5568	86	563	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	76.5544	101	563	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_002163085.1	s__41-12-T18 sp002163085	76.4813	87	563	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	76.3516	79	563	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 23:15:13,081] [INFO] GTDB search result was written to OceanDNA-b36275/result_gtdb.tsv
[2023-03-18 23:15:13,082] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:15:13,083] [INFO] DFAST_QC result json was written to OceanDNA-b36275/dqc_result.json
[2023-03-18 23:15:13,083] [INFO] DFAST_QC completed!
[2023-03-18 23:15:13,083] [INFO] Total running time: 0h1m0s