[2023-03-15 21:48:06,705] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,705] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference
[2023-03-15 21:48:07,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,860] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,860] [INFO] Running command: cat /var/lib/cwl/stgf2a55ab7-4d61-4900-b42c-e50381282c9d/OceanDNA-b310.fa | prodigal -d OceanDNA-b310/cds.fna -a OceanDNA-b310/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:18,214] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:18,214] [INFO] Task started: HMMsearch
[2023-03-15 21:48:18,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b310/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/reference_markers.hmm OceanDNA-b310/protein.faa > /dev/null
[2023-03-15 21:48:18,374] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:18,375] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf2a55ab7-4d61-4900-b42c-e50381282c9d/OceanDNA-b310.fa]
[2023-03-15 21:48:18,391] [INFO] Query marker FASTA was written to OceanDNA-b310/markers.fasta
[2023-03-15 21:48:18,392] [INFO] Task started: Blastn
[2023-03-15 21:48:18,392] [INFO] Running command: blastn -query OceanDNA-b310/markers.fasta -db /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/reference_markers.fasta -out OceanDNA-b310/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:18,928] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:18,930] [INFO] Selected 14 target genomes.
[2023-03-15 21:48:18,930] [INFO] Target genome list was writen to OceanDNA-b310/target_genomes.txt
[2023-03-15 21:48:18,937] [INFO] Task started: fastANI
[2023-03-15 21:48:18,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a55ab7-4d61-4900-b42c-e50381282c9d/OceanDNA-b310.fa --refList OceanDNA-b310/target_genomes.txt --output OceanDNA-b310/fastani_result.tsv --threads 1
[2023-03-15 21:48:27,122] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:27,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:27,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:27,123] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:27,123] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:27,123] [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 21:48:27,123] [INFO] DFAST Taxonomy check result was written to OceanDNA-b310/tc_result.tsv
[2023-03-15 21:48:27,123] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:27,123] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:27,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/checkm_data
[2023-03-15 21:48:27,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:27,151] [INFO] Task started: CheckM
[2023-03-15 21:48:27,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b310/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b310/checkm_input OceanDNA-b310/checkm_result
[2023-03-15 21:48:57,149] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:57,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:57,172] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:57,172] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:57,173] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b310/markers.fasta)
[2023-03-15 21:48:57,174] [INFO] Task started: Blastn
[2023-03-15 21:48:57,174] [INFO] Running command: blastn -query OceanDNA-b310/markers.fasta -db /var/lib/cwl/stgf79a6449-df1d-41d6-8392-e8e2d033f4ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b310/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:57,949] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:57,955] [INFO] Selected 17 target genomes.
[2023-03-15 21:48:57,955] [INFO] Target genome list was writen to OceanDNA-b310/target_genomes_gtdb.txt
[2023-03-15 21:48:57,967] [INFO] Task started: fastANI
[2023-03-15 21:48:57,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a55ab7-4d61-4900-b42c-e50381282c9d/OceanDNA-b310.fa --refList OceanDNA-b310/target_genomes_gtdb.txt --output OceanDNA-b310/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:11,222] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:11,228] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:49:11,229] [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	98.3684	422	524	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002712885.1	s__UBA8438 sp002712885	77.5501	114	524	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	76.7808	111	524	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.4653	98	524	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	75.7493	59	524	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_011523845.1	s__WTFV01 sp011523845	75.5996	51	524	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:11,229] [INFO] GTDB search result was written to OceanDNA-b310/result_gtdb.tsv
[2023-03-15 21:49:11,229] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:11,230] [INFO] DFAST_QC result json was written to OceanDNA-b310/dqc_result.json
[2023-03-15 21:49:11,230] [INFO] DFAST_QC completed!
[2023-03-15 21:49:11,230] [INFO] Total running time: 0h1m5s