[2023-03-16 08:10:35,104] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,107] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,107] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference
[2023-03-16 08:10:36,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,244] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,245] [INFO] Running command: cat /var/lib/cwl/stgddefc36d-c07e-4e0f-8c25-58d41402a7eb/OceanDNA-b13138.fa | prodigal -d OceanDNA-b13138/cds.fna -a OceanDNA-b13138/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:54,532] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:54,532] [INFO] Task started: HMMsearch
[2023-03-16 08:10:54,532] [INFO] Running command: hmmsearch --tblout OceanDNA-b13138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/reference_markers.hmm OceanDNA-b13138/protein.faa > /dev/null
[2023-03-16 08:10:54,751] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:54,751] [INFO] Found 6/6 markers.
[2023-03-16 08:10:54,821] [INFO] Query marker FASTA was written to OceanDNA-b13138/markers.fasta
[2023-03-16 08:10:54,822] [INFO] Task started: Blastn
[2023-03-16 08:10:54,822] [INFO] Running command: blastn -query OceanDNA-b13138/markers.fasta -db /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/reference_markers.fasta -out OceanDNA-b13138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:55,339] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:55,352] [INFO] Selected 20 target genomes.
[2023-03-16 08:10:55,352] [INFO] Target genome list was writen to OceanDNA-b13138/target_genomes.txt
[2023-03-16 08:10:55,366] [INFO] Task started: fastANI
[2023-03-16 08:10:55,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgddefc36d-c07e-4e0f-8c25-58d41402a7eb/OceanDNA-b13138.fa --refList OceanDNA-b13138/target_genomes.txt --output OceanDNA-b13138/fastani_result.tsv --threads 1
[2023-03-16 08:11:06,291] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:06,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:06,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:06,294] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:06,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:11:06,294] [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
Halobacteriovorax vibrionivorans	strain=BL9	GCA_003346865.1	2152716	2152716	type	True	75.6788	54	1181	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:11:06,299] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13138/tc_result.tsv
[2023-03-16 08:11:06,307] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:06,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:06,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/checkm_data
[2023-03-16 08:11:06,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:06,371] [INFO] Task started: CheckM
[2023-03-16 08:11:06,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13138/checkm_input OceanDNA-b13138/checkm_result
[2023-03-16 08:11:53,846] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:53,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:53,896] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:53,897] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:53,897] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13138/markers.fasta)
[2023-03-16 08:11:53,898] [INFO] Task started: Blastn
[2023-03-16 08:11:53,898] [INFO] Running command: blastn -query OceanDNA-b13138/markers.fasta -db /var/lib/cwl/stgb1a1bad5-fe9d-407e-a1de-89692b49c9c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:54,668] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:54,685] [INFO] Selected 20 target genomes.
[2023-03-16 08:11:54,685] [INFO] Target genome list was writen to OceanDNA-b13138/target_genomes_gtdb.txt
[2023-03-16 08:11:54,702] [INFO] Task started: fastANI
[2023-03-16 08:11:54,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgddefc36d-c07e-4e0f-8c25-58d41402a7eb/OceanDNA-b13138.fa --refList OceanDNA-b13138/target_genomes_gtdb.txt --output OceanDNA-b13138/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:12:05,058] [INFO] Task succeeded: fastANI
[2023-03-16 08:12:05,065] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:12:05,065] [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_002753895.1	s__Halobacteriovorax sp002753895	78.4385	58	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707495.1	s__GCA-2707495 sp002707495	77.6105	77	1181	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_002718735.1	s__UBA845 sp002718735	76.5861	56	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA845	95.0	99.20	98.78	0.71	0.69	3	-
GCA_002706205.1	s__GCA-2706205 sp002706205	76.5286	83	1181	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_002711995.1	s__UBA845 sp002711995	76.5152	84	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA845	95.0	99.96	99.96	0.99	0.99	4	-
GCF_000447795.1	s__DB6-IX sp000447795	76.279	59	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713145.1	s__GCA-2713145 sp002713145	76.2395	96	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2713145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663815.1	s__GCA-2706205 sp018663815	75.9586	51	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2706205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612895.1	s__DB6-IX sp003612895	75.6397	53	1181	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	98.61	98.58	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-16 08:12:05,070] [INFO] GTDB search result was written to OceanDNA-b13138/result_gtdb.tsv
[2023-03-16 08:12:05,076] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:12:05,082] [INFO] DFAST_QC result json was written to OceanDNA-b13138/dqc_result.json
[2023-03-16 08:12:05,082] [INFO] DFAST_QC completed!
[2023-03-16 08:12:05,082] [INFO] Total running time: 0h1m30s