[2023-03-16 04:54:07,037] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,038] [INFO] DQC Reference Directory: /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference
[2023-03-16 04:54:08,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,335] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,335] [INFO] Running command: cat /var/lib/cwl/stgb083f04f-4a0b-4a34-b343-9be598d9746c/OceanDNA-b13149.fa | prodigal -d OceanDNA-b13149/cds.fna -a OceanDNA-b13149/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:23,119] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:23,119] [INFO] Task started: HMMsearch
[2023-03-16 04:54:23,119] [INFO] Running command: hmmsearch --tblout OceanDNA-b13149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/reference_markers.hmm OceanDNA-b13149/protein.faa > /dev/null
[2023-03-16 04:54:23,425] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:23,426] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb083f04f-4a0b-4a34-b343-9be598d9746c/OceanDNA-b13149.fa]
[2023-03-16 04:54:23,453] [INFO] Query marker FASTA was written to OceanDNA-b13149/markers.fasta
[2023-03-16 04:54:23,453] [INFO] Task started: Blastn
[2023-03-16 04:54:23,453] [INFO] Running command: blastn -query OceanDNA-b13149/markers.fasta -db /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/reference_markers.fasta -out OceanDNA-b13149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:23,999] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:24,000] [INFO] Selected 18 target genomes.
[2023-03-16 04:54:24,000] [INFO] Target genome list was writen to OceanDNA-b13149/target_genomes.txt
[2023-03-16 04:54:24,011] [INFO] Task started: fastANI
[2023-03-16 04:54:24,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgb083f04f-4a0b-4a34-b343-9be598d9746c/OceanDNA-b13149.fa --refList OceanDNA-b13149/target_genomes.txt --output OceanDNA-b13149/fastani_result.tsv --threads 1
[2023-03-16 04:54:32,604] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:32,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:32,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:32,605] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:32,605] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:32,605] [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 04:54:32,605] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13149/tc_result.tsv
[2023-03-16 04:54:32,605] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:32,606] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:32,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/checkm_data
[2023-03-16 04:54:32,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:32,620] [INFO] Task started: CheckM
[2023-03-16 04:54:32,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13149/checkm_input OceanDNA-b13149/checkm_result
[2023-03-16 04:55:13,663] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:13,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:13,666] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:13,666] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:13,666] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13149/markers.fasta)
[2023-03-16 04:55:13,667] [INFO] Task started: Blastn
[2023-03-16 04:55:13,668] [INFO] Running command: blastn -query OceanDNA-b13149/markers.fasta -db /var/lib/cwl/stge5d92682-2d3b-40e1-96ee-84658894e7b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:14,404] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:14,405] [INFO] Selected 23 target genomes.
[2023-03-16 04:55:14,405] [INFO] Target genome list was writen to OceanDNA-b13149/target_genomes_gtdb.txt
[2023-03-16 04:55:14,454] [INFO] Task started: fastANI
[2023-03-16 04:55:14,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgb083f04f-4a0b-4a34-b343-9be598d9746c/OceanDNA-b13149.fa --refList OceanDNA-b13149/target_genomes_gtdb.txt --output OceanDNA-b13149/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:25,496] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:25,500] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:25,500] [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_002706205.1	s__GCA-2706205 sp002706205	99.2928	752	962	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2706205	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018663815.1	s__GCA-2706205 sp018663815	76.7084	79	962	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2706205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707495.1	s__GCA-2707495 sp002707495	76.56	66	962	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2707495	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713145.1	s__GCA-2713145 sp002713145	76.2152	82	962	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2713145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:25,500] [INFO] GTDB search result was written to OceanDNA-b13149/result_gtdb.tsv
[2023-03-16 04:55:25,500] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:25,501] [INFO] DFAST_QC result json was written to OceanDNA-b13149/dqc_result.json
[2023-03-16 04:55:25,501] [INFO] DFAST_QC completed!
[2023-03-16 04:55:25,501] [INFO] Total running time: 0h1m18s