[2023-03-16 18:09:00,095] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:09:00,095] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:09:00,095] [INFO] DQC Reference Directory: /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference
[2023-03-16 18:09:01,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:09:01,206] [INFO] Task started: Prodigal
[2023-03-16 18:09:01,206] [INFO] Running command: cat /var/lib/cwl/stg94185445-faf0-4b81-be38-a9db8171c9d7/OceanDNA-b264.fa | prodigal -d OceanDNA-b264/cds.fna -a OceanDNA-b264/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:09:22,514] [INFO] Task succeeded: Prodigal
[2023-03-16 18:09:22,514] [INFO] Task started: HMMsearch
[2023-03-16 18:09:22,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b264/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/reference_markers.hmm OceanDNA-b264/protein.faa > /dev/null
[2023-03-16 18:09:22,715] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:09:22,715] [INFO] Found 6/6 markers.
[2023-03-16 18:09:22,736] [INFO] Query marker FASTA was written to OceanDNA-b264/markers.fasta
[2023-03-16 18:09:22,738] [INFO] Task started: Blastn
[2023-03-16 18:09:22,738] [INFO] Running command: blastn -query OceanDNA-b264/markers.fasta -db /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/reference_markers.fasta -out OceanDNA-b264/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:23,266] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:23,267] [INFO] Selected 25 target genomes.
[2023-03-16 18:09:23,267] [INFO] Target genome list was writen to OceanDNA-b264/target_genomes.txt
[2023-03-16 18:09:23,298] [INFO] Task started: fastANI
[2023-03-16 18:09:23,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg94185445-faf0-4b81-be38-a9db8171c9d7/OceanDNA-b264.fa --refList OceanDNA-b264/target_genomes.txt --output OceanDNA-b264/fastani_result.tsv --threads 1
[2023-03-16 18:09:40,816] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:40,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:09:40,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:09:40,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:09:40,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:09:40,817] [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
--------------------------------------------------------------------------------
[2023-03-16 18:09:40,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b264/tc_result.tsv
[2023-03-16 18:09:40,817] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:09:40,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:09:40,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/checkm_data
[2023-03-16 18:09:40,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:09:41,021] [INFO] Task started: CheckM
[2023-03-16 18:09:41,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b264/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b264/checkm_input OceanDNA-b264/checkm_result
[2023-03-16 18:10:50,605] [INFO] Task succeeded: CheckM
[2023-03-16 18:10:50,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:10:50,609] [INFO] ===== Completeness check finished =====
[2023-03-16 18:10:50,609] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:10:50,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b264/markers.fasta)
[2023-03-16 18:10:50,611] [INFO] Task started: Blastn
[2023-03-16 18:10:50,611] [INFO] Running command: blastn -query OceanDNA-b264/markers.fasta -db /var/lib/cwl/stga8ba6e83-269d-4cc5-b4b2-cc97ea6349ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b264/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:10:52,540] [INFO] Task succeeded: Blastn
[2023-03-16 18:10:52,541] [INFO] Selected 29 target genomes.
[2023-03-16 18:10:52,541] [INFO] Target genome list was writen to OceanDNA-b264/target_genomes_gtdb.txt
[2023-03-16 18:10:52,873] [INFO] Task started: fastANI
[2023-03-16 18:10:52,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg94185445-faf0-4b81-be38-a9db8171c9d7/OceanDNA-b264.fa --refList OceanDNA-b264/target_genomes_gtdb.txt --output OceanDNA-b264/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:11:20,589] [INFO] Task succeeded: fastANI
[2023-03-16 18:11:20,594] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:11:20,594] [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_002347025.1	s__UBA2990 sp002347025	77.8306	226	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2990	95.0	99.94	99.92	0.88	0.83	3	-
GCA_003533545.1	s__UBA9620 sp003533545	76.8722	89	1142	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	76.7661	152	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.2478	108	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_002726085.1	s__NP936 sp002726085	76.2433	166	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	75.5137	52	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	75.4761	66	1142	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:11:20,594] [INFO] GTDB search result was written to OceanDNA-b264/result_gtdb.tsv
[2023-03-16 18:11:20,595] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:11:20,596] [INFO] DFAST_QC result json was written to OceanDNA-b264/dqc_result.json
[2023-03-16 18:11:20,596] [INFO] DFAST_QC completed!
[2023-03-16 18:11:20,596] [INFO] Total running time: 0h2m21s