[2023-03-15 04:01:38,384] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:01:38,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:01:38,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference
[2023-03-15 04:01:39,526] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:01:39,526] [INFO] Task started: Prodigal
[2023-03-15 04:01:39,526] [INFO] Running command: cat /var/lib/cwl/stge800e5b7-2826-43b5-98d9-ac4000bb24d6/OceanDNA-b40857.fa | prodigal -d OceanDNA-b40857/cds.fna -a OceanDNA-b40857/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:01:51,546] [INFO] Task succeeded: Prodigal
[2023-03-15 04:01:51,546] [INFO] Task started: HMMsearch
[2023-03-15 04:01:51,546] [INFO] Running command: hmmsearch --tblout OceanDNA-b40857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/reference_markers.hmm OceanDNA-b40857/protein.faa > /dev/null
[2023-03-15 04:01:51,740] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:01:51,741] [INFO] Found 6/6 markers.
[2023-03-15 04:01:51,758] [INFO] Query marker FASTA was written to OceanDNA-b40857/markers.fasta
[2023-03-15 04:01:51,759] [INFO] Task started: Blastn
[2023-03-15 04:01:51,759] [INFO] Running command: blastn -query OceanDNA-b40857/markers.fasta -db /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/reference_markers.fasta -out OceanDNA-b40857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:01:52,319] [INFO] Task succeeded: Blastn
[2023-03-15 04:01:52,320] [INFO] Selected 18 target genomes.
[2023-03-15 04:01:52,320] [INFO] Target genome list was writen to OceanDNA-b40857/target_genomes.txt
[2023-03-15 04:01:52,331] [INFO] Task started: fastANI
[2023-03-15 04:01:52,331] [INFO] Running command: fastANI --query /var/lib/cwl/stge800e5b7-2826-43b5-98d9-ac4000bb24d6/OceanDNA-b40857.fa --refList OceanDNA-b40857/target_genomes.txt --output OceanDNA-b40857/fastani_result.tsv --threads 1
[2023-03-15 04:02:03,281] [INFO] Task succeeded: fastANI
[2023-03-15 04:02:03,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:02:03,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:02:03,282] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:02:03,282] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:02:03,282] [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
--------------------------------------------------------------------------------
[2023-03-15 04:02:03,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40857/tc_result.tsv
[2023-03-15 04:02:03,285] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:02:03,285] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:02:03,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/checkm_data
[2023-03-15 04:02:03,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:02:03,292] [INFO] Task started: CheckM
[2023-03-15 04:02:03,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40857/checkm_input OceanDNA-b40857/checkm_result
[2023-03-15 04:02:37,058] [INFO] Task succeeded: CheckM
[2023-03-15 04:02:37,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:02:37,068] [INFO] ===== Completeness check finished =====
[2023-03-15 04:02:37,068] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:02:37,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40857/markers.fasta)
[2023-03-15 04:02:37,069] [INFO] Task started: Blastn
[2023-03-15 04:02:37,070] [INFO] Running command: blastn -query OceanDNA-b40857/markers.fasta -db /var/lib/cwl/stg851777ce-2259-4c43-85a7-0d23339db5e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:02:37,998] [INFO] Task succeeded: Blastn
[2023-03-15 04:02:38,002] [INFO] Selected 26 target genomes.
[2023-03-15 04:02:38,002] [INFO] Target genome list was writen to OceanDNA-b40857/target_genomes_gtdb.txt
[2023-03-15 04:02:38,036] [INFO] Task started: fastANI
[2023-03-15 04:02:38,036] [INFO] Running command: fastANI --query /var/lib/cwl/stge800e5b7-2826-43b5-98d9-ac4000bb24d6/OceanDNA-b40857.fa --refList OceanDNA-b40857/target_genomes_gtdb.txt --output OceanDNA-b40857/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:02:51,223] [INFO] Task succeeded: fastANI
[2023-03-15 04:02:51,226] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:02:51,227] [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_002712055.1	s__UBA9145 sp002712055	99.157	541	701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.31	99.25	0.77	0.70	5	conclusive
GCA_002694855.1	s__UBA9145 sp002694855	81.7176	429	701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.18	97.28	0.74	0.66	6	-
GCA_002377605.1	s__UBA9145 sp002377605	77.6684	51	701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960305.1	s__UBA9145 sp012960305	77.2283	51	701	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:02:51,228] [INFO] GTDB search result was written to OceanDNA-b40857/result_gtdb.tsv
[2023-03-15 04:02:51,230] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:02:51,232] [INFO] DFAST_QC result json was written to OceanDNA-b40857/dqc_result.json
[2023-03-15 04:02:51,232] [INFO] DFAST_QC completed!
[2023-03-15 04:02:51,232] [INFO] Total running time: 0h1m13s