[2023-03-18 09:42:02,251] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:42:02,251] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:42:02,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference
[2023-03-18 09:42:03,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:42:03,333] [INFO] Task started: Prodigal
[2023-03-18 09:42:03,333] [INFO] Running command: cat /var/lib/cwl/stg8131eec5-5ab3-4972-bc9d-b68f09945f02/OceanDNA-b38153.fa | prodigal -d OceanDNA-b38153/cds.fna -a OceanDNA-b38153/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:42:17,393] [INFO] Task succeeded: Prodigal
[2023-03-18 09:42:17,394] [INFO] Task started: HMMsearch
[2023-03-18 09:42:17,394] [INFO] Running command: hmmsearch --tblout OceanDNA-b38153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/reference_markers.hmm OceanDNA-b38153/protein.faa > /dev/null
[2023-03-18 09:42:17,556] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:42:17,556] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8131eec5-5ab3-4972-bc9d-b68f09945f02/OceanDNA-b38153.fa]
[2023-03-18 09:42:17,571] [INFO] Query marker FASTA was written to OceanDNA-b38153/markers.fasta
[2023-03-18 09:42:17,572] [INFO] Task started: Blastn
[2023-03-18 09:42:17,572] [INFO] Running command: blastn -query OceanDNA-b38153/markers.fasta -db /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/reference_markers.fasta -out OceanDNA-b38153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:18,118] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:18,119] [INFO] Selected 24 target genomes.
[2023-03-18 09:42:18,119] [INFO] Target genome list was writen to OceanDNA-b38153/target_genomes.txt
[2023-03-18 09:42:18,132] [INFO] Task started: fastANI
[2023-03-18 09:42:18,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg8131eec5-5ab3-4972-bc9d-b68f09945f02/OceanDNA-b38153.fa --refList OceanDNA-b38153/target_genomes.txt --output OceanDNA-b38153/fastani_result.tsv --threads 1
[2023-03-18 09:42:32,162] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:32,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:42:32,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:42:32,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:42:32,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:42:32,163] [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
--------------------------------------------------------------------------------
[2023-03-18 09:42:32,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38153/tc_result.tsv
[2023-03-18 09:42:32,164] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:42:32,164] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:42:32,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/checkm_data
[2023-03-18 09:42:32,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:42:32,177] [INFO] Task started: CheckM
[2023-03-18 09:42:32,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38153/checkm_input OceanDNA-b38153/checkm_result
[2023-03-18 09:43:10,187] [INFO] Task succeeded: CheckM
[2023-03-18 09:43:10,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:43:10,189] [INFO] ===== Completeness check finished =====
[2023-03-18 09:43:10,189] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:43:10,189] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38153/markers.fasta)
[2023-03-18 09:43:10,191] [INFO] Task started: Blastn
[2023-03-18 09:43:10,191] [INFO] Running command: blastn -query OceanDNA-b38153/markers.fasta -db /var/lib/cwl/stg716a310c-d4c4-4e14-b861-35e4fbf4542a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:43:11,009] [INFO] Task succeeded: Blastn
[2023-03-18 09:43:11,010] [INFO] Selected 12 target genomes.
[2023-03-18 09:43:11,010] [INFO] Target genome list was writen to OceanDNA-b38153/target_genomes_gtdb.txt
[2023-03-18 09:43:11,043] [INFO] Task started: fastANI
[2023-03-18 09:43:11,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg8131eec5-5ab3-4972-bc9d-b68f09945f02/OceanDNA-b38153.fa --refList OceanDNA-b38153/target_genomes_gtdb.txt --output OceanDNA-b38153/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:43:15,737] [INFO] Task succeeded: fastANI
[2023-03-18 09:43:15,744] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:43:15,744] [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_002721785.1	s__Luminiphilus sp002721785	99.7677	702	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	conclusive
GCA_902631395.1	s__Luminiphilus sp902631395	81.4202	360	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.59	98.59	0.74	0.74	2	-
GCA_902520195.1	s__Luminiphilus sp902520195	78.6054	177	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_902623175.1	s__Luminiphilus sp902623175	78.0699	193	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	77.9594	140	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911345.1	s__Luminiphilus sp013911345	77.9471	81	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	77.6514	137	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683395.1	s__Luminiphilus sp002683395	77.1067	148	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
GCA_002705465.1	s__Luminiphilus sp002705465	77.0831	79	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377985.1	s__Luminiphilus sp002377985	76.8447	118	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523115.1	s__Luminiphilus sp011523115	76.7947	120	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:43:15,744] [INFO] GTDB search result was written to OceanDNA-b38153/result_gtdb.tsv
[2023-03-18 09:43:15,745] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:43:15,745] [INFO] DFAST_QC result json was written to OceanDNA-b38153/dqc_result.json
[2023-03-18 09:43:15,746] [INFO] DFAST_QC completed!
[2023-03-18 09:43:15,746] [INFO] Total running time: 0h1m13s