[2023-03-18 09:19:06,941] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:19:06,941] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:19:06,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference
[2023-03-18 09:19:08,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:19:08,109] [INFO] Task started: Prodigal
[2023-03-18 09:19:08,109] [INFO] Running command: cat /var/lib/cwl/stg60034c40-3608-45fc-bcfb-25e4b8c9eee9/OceanDNA-b276.fa | prodigal -d OceanDNA-b276/cds.fna -a OceanDNA-b276/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:19:29,956] [INFO] Task succeeded: Prodigal
[2023-03-18 09:19:29,956] [INFO] Task started: HMMsearch
[2023-03-18 09:19:29,956] [INFO] Running command: hmmsearch --tblout OceanDNA-b276/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/reference_markers.hmm OceanDNA-b276/protein.faa > /dev/null
[2023-03-18 09:19:30,153] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:19:30,154] [INFO] Found 6/6 markers.
[2023-03-18 09:19:30,180] [INFO] Query marker FASTA was written to OceanDNA-b276/markers.fasta
[2023-03-18 09:19:30,181] [INFO] Task started: Blastn
[2023-03-18 09:19:30,181] [INFO] Running command: blastn -query OceanDNA-b276/markers.fasta -db /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/reference_markers.fasta -out OceanDNA-b276/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:19:30,709] [INFO] Task succeeded: Blastn
[2023-03-18 09:19:30,715] [INFO] Selected 13 target genomes.
[2023-03-18 09:19:30,715] [INFO] Target genome list was writen to OceanDNA-b276/target_genomes.txt
[2023-03-18 09:19:30,745] [INFO] Task started: fastANI
[2023-03-18 09:19:30,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg60034c40-3608-45fc-bcfb-25e4b8c9eee9/OceanDNA-b276.fa --refList OceanDNA-b276/target_genomes.txt --output OceanDNA-b276/fastani_result.tsv --threads 1
[2023-03-18 09:19:38,522] [INFO] Task succeeded: fastANI
[2023-03-18 09:19:38,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:19:38,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:19:38,523] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:19:38,523] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:19:38,523] [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 09:19:38,525] [INFO] DFAST Taxonomy check result was written to OceanDNA-b276/tc_result.tsv
[2023-03-18 09:19:38,527] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:19:38,527] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:19:38,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/checkm_data
[2023-03-18 09:19:38,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:19:38,537] [INFO] Task started: CheckM
[2023-03-18 09:19:38,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b276/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b276/checkm_input OceanDNA-b276/checkm_result
[2023-03-18 09:20:32,893] [INFO] Task succeeded: CheckM
[2023-03-18 09:20:32,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:20:32,938] [INFO] ===== Completeness check finished =====
[2023-03-18 09:20:32,938] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:20:32,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b276/markers.fasta)
[2023-03-18 09:20:32,940] [INFO] Task started: Blastn
[2023-03-18 09:20:32,940] [INFO] Running command: blastn -query OceanDNA-b276/markers.fasta -db /var/lib/cwl/stg918611dd-492d-4766-9c03-4979fc35d948/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b276/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:20:33,694] [INFO] Task succeeded: Blastn
[2023-03-18 09:20:33,698] [INFO] Selected 19 target genomes.
[2023-03-18 09:20:33,698] [INFO] Target genome list was writen to OceanDNA-b276/target_genomes_gtdb.txt
[2023-03-18 09:20:33,897] [INFO] Task started: fastANI
[2023-03-18 09:20:33,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg60034c40-3608-45fc-bcfb-25e4b8c9eee9/OceanDNA-b276.fa --refList OceanDNA-b276/target_genomes_gtdb.txt --output OceanDNA-b276/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:20:46,169] [INFO] Task succeeded: fastANI
[2023-03-18 09:20:46,174] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:20:46,174] [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_003533545.1	s__UBA9620 sp003533545	92.0515	627	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	77.6456	197	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712885.1	s__UBA8438 sp002712885	77.4926	195	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.633	211	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.0604	134	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	75.7745	100	1177	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:20:46,176] [INFO] GTDB search result was written to OceanDNA-b276/result_gtdb.tsv
[2023-03-18 09:20:46,178] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:20:46,181] [INFO] DFAST_QC result json was written to OceanDNA-b276/dqc_result.json
[2023-03-18 09:20:46,181] [INFO] DFAST_QC completed!
[2023-03-18 09:20:46,181] [INFO] Total running time: 0h1m39s