[2023-03-15 10:52:57,300] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,300] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference
[2023-03-15 10:52:58,877] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,878] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,878] [INFO] Running command: cat /var/lib/cwl/stg90dfe60d-fe59-448b-9f3d-9ed2112afbd4/OceanDNA-b46402.fa | prodigal -d OceanDNA-b46402/cds.fna -a OceanDNA-b46402/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:28,133] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:28,134] [INFO] Task started: HMMsearch
[2023-03-15 10:53:28,134] [INFO] Running command: hmmsearch --tblout OceanDNA-b46402/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/reference_markers.hmm OceanDNA-b46402/protein.faa > /dev/null
[2023-03-15 10:53:28,338] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:28,339] [INFO] Found 6/6 markers.
[2023-03-15 10:53:28,361] [INFO] Query marker FASTA was written to OceanDNA-b46402/markers.fasta
[2023-03-15 10:53:28,362] [INFO] Task started: Blastn
[2023-03-15 10:53:28,362] [INFO] Running command: blastn -query OceanDNA-b46402/markers.fasta -db /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/reference_markers.fasta -out OceanDNA-b46402/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:28,931] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:28,997] [INFO] Selected 36 target genomes.
[2023-03-15 10:53:28,997] [INFO] Target genome list was writen to OceanDNA-b46402/target_genomes.txt
[2023-03-15 10:53:29,021] [INFO] Task started: fastANI
[2023-03-15 10:53:29,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg90dfe60d-fe59-448b-9f3d-9ed2112afbd4/OceanDNA-b46402.fa --refList OceanDNA-b46402/target_genomes.txt --output OceanDNA-b46402/fastani_result.tsv --threads 1
[2023-03-15 10:53:55,191] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:55,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:55,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:55,194] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:55,194] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:55,195] [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
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	74.7447	51	939	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:55,195] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46402/tc_result.tsv
[2023-03-15 10:53:55,195] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:55,195] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:55,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/checkm_data
[2023-03-15 10:53:55,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:55,383] [INFO] Task started: CheckM
[2023-03-15 10:53:55,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46402/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46402/checkm_input OceanDNA-b46402/checkm_result
[2023-03-15 10:55:07,736] [INFO] Task succeeded: CheckM
[2023-03-15 10:55:07,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.14%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 10:55:07,739] [INFO] ===== Completeness check finished =====
[2023-03-15 10:55:07,739] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:55:07,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46402/markers.fasta)
[2023-03-15 10:55:07,740] [INFO] Task started: Blastn
[2023-03-15 10:55:07,741] [INFO] Running command: blastn -query OceanDNA-b46402/markers.fasta -db /var/lib/cwl/stg201ab1be-bfc8-4a8c-8ace-cebc477a7ab6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46402/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:55:08,563] [INFO] Task succeeded: Blastn
[2023-03-15 10:55:08,563] [INFO] Selected 8 target genomes.
[2023-03-15 10:55:08,563] [INFO] Target genome list was writen to OceanDNA-b46402/target_genomes_gtdb.txt
[2023-03-15 10:55:08,568] [INFO] Task started: fastANI
[2023-03-15 10:55:08,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg90dfe60d-fe59-448b-9f3d-9ed2112afbd4/OceanDNA-b46402.fa --refList OceanDNA-b46402/target_genomes_gtdb.txt --output OceanDNA-b46402/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:55:14,105] [INFO] Task succeeded: fastANI
[2023-03-15 10:55:14,110] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:55:14,111] [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_015658765.1	s__UBA1096 sp015658765	89.5454	429	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674955.1	s__UBA1096 sp018674955	88.3104	676	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	-
GCA_003972865.1	s__UBA1096 sp003972865	86.5909	511	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	85.7511	479	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	85.1827	725	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	83.1493	613	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453165.1	s__UBA1096 sp002453165	79.1646	350	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
GCA_011523195.1	s__UBA1096 sp011523195	78.8985	285	939	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:55:14,111] [INFO] GTDB search result was written to OceanDNA-b46402/result_gtdb.tsv
[2023-03-15 10:55:14,111] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:55:14,112] [INFO] DFAST_QC result json was written to OceanDNA-b46402/dqc_result.json
[2023-03-15 10:55:14,112] [INFO] DFAST_QC completed!
[2023-03-15 10:55:14,112] [INFO] Total running time: 0h2m17s