[2023-03-19 04:29:38,147] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference
[2023-03-19 04:29:39,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,841] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,841] [INFO] Running command: cat /var/lib/cwl/stg87237329-0ae1-41ae-843f-ef1da2ca3cf6/OceanDNA-b23249.fa | prodigal -d OceanDNA-b23249/cds.fna -a OceanDNA-b23249/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:02,153] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:02,153] [INFO] Task started: HMMsearch
[2023-03-19 04:30:02,153] [INFO] Running command: hmmsearch --tblout OceanDNA-b23249/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/reference_markers.hmm OceanDNA-b23249/protein.faa > /dev/null
[2023-03-19 04:30:02,368] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:02,369] [INFO] Found 6/6 markers.
[2023-03-19 04:30:02,396] [INFO] Query marker FASTA was written to OceanDNA-b23249/markers.fasta
[2023-03-19 04:30:02,396] [INFO] Task started: Blastn
[2023-03-19 04:30:02,396] [INFO] Running command: blastn -query OceanDNA-b23249/markers.fasta -db /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/reference_markers.fasta -out OceanDNA-b23249/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:02,895] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:02,896] [INFO] Selected 6 target genomes.
[2023-03-19 04:30:02,896] [INFO] Target genome list was writen to OceanDNA-b23249/target_genomes.txt
[2023-03-19 04:30:02,899] [INFO] Task started: fastANI
[2023-03-19 04:30:02,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg87237329-0ae1-41ae-843f-ef1da2ca3cf6/OceanDNA-b23249.fa --refList OceanDNA-b23249/target_genomes.txt --output OceanDNA-b23249/fastani_result.tsv --threads 1
[2023-03-19 04:30:06,306] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:06,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:06,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:06,306] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:06,306] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:06,306] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:06,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23249/tc_result.tsv
[2023-03-19 04:30:06,307] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:06,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:06,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/checkm_data
[2023-03-19 04:30:06,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:06,316] [INFO] Task started: CheckM
[2023-03-19 04:30:06,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23249/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23249/checkm_input OceanDNA-b23249/checkm_result
[2023-03-19 04:31:02,675] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:02,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:02,678] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:02,678] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:02,678] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23249/markers.fasta)
[2023-03-19 04:31:02,678] [INFO] Task started: Blastn
[2023-03-19 04:31:02,679] [INFO] Running command: blastn -query OceanDNA-b23249/markers.fasta -db /var/lib/cwl/stg0fd4f298-4d87-447e-9345-734d6eedb116/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23249/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:03,383] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:03,384] [INFO] Selected 11 target genomes.
[2023-03-19 04:31:03,384] [INFO] Target genome list was writen to OceanDNA-b23249/target_genomes_gtdb.txt
[2023-03-19 04:31:03,416] [INFO] Task started: fastANI
[2023-03-19 04:31:03,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg87237329-0ae1-41ae-843f-ef1da2ca3cf6/OceanDNA-b23249.fa --refList OceanDNA-b23249/target_genomes_gtdb.txt --output OceanDNA-b23249/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:11,417] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:11,419] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:31:11,420] [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_002709695.1	s__UBA9662 sp002709695	99.2673	1201	1339	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697225.1	s__UBA9662 sp002697225	84.2806	852	1339	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	97.07	96.17	0.75	0.62	4	-
GCA_012963885.1	s__UBA9662 sp012963885	80.2831	948	1339	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	99.64	99.54	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:11,420] [INFO] GTDB search result was written to OceanDNA-b23249/result_gtdb.tsv
[2023-03-19 04:31:11,420] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:11,420] [INFO] DFAST_QC result json was written to OceanDNA-b23249/dqc_result.json
[2023-03-19 04:31:11,421] [INFO] DFAST_QC completed!
[2023-03-19 04:31:11,421] [INFO] Total running time: 0h1m33s