[2023-03-15 21:01:44,384] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stgef7230a1-9be3-4ccd-b1a1-878ca1769606/OceanDNA-b30.fa | prodigal -d OceanDNA-b30/cds.fna -a OceanDNA-b30/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:13,876] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:13,876] [INFO] Task started: HMMsearch
[2023-03-15 21:02:13,876] [INFO] Running command: hmmsearch --tblout OceanDNA-b30/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/reference_markers.hmm OceanDNA-b30/protein.faa > /dev/null
[2023-03-15 21:02:14,105] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:14,106] [INFO] Found 6/6 markers.
[2023-03-15 21:02:14,138] [INFO] Query marker FASTA was written to OceanDNA-b30/markers.fasta
[2023-03-15 21:02:14,138] [INFO] Task started: Blastn
[2023-03-15 21:02:14,138] [INFO] Running command: blastn -query OceanDNA-b30/markers.fasta -db /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/reference_markers.fasta -out OceanDNA-b30/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:14,673] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:14,674] [INFO] Selected 15 target genomes.
[2023-03-15 21:02:14,674] [INFO] Target genome list was writen to OceanDNA-b30/target_genomes.txt
[2023-03-15 21:02:14,682] [INFO] Task started: fastANI
[2023-03-15 21:02:14,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7230a1-9be3-4ccd-b1a1-878ca1769606/OceanDNA-b30.fa --refList OceanDNA-b30/target_genomes.txt --output OceanDNA-b30/fastani_result.tsv --threads 1
[2023-03-15 21:02:26,554] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:26,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:26,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:26,558] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:26,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:26,558] [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
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	74.5588	53	1565	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:26,558] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30/tc_result.tsv
[2023-03-15 21:02:26,558] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:26,559] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:26,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/checkm_data
[2023-03-15 21:02:26,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:26,566] [INFO] Task started: CheckM
[2023-03-15 21:02:26,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30/checkm_input OceanDNA-b30/checkm_result
[2023-03-15 21:03:34,752] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:34,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:34,756] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:34,756] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:34,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30/markers.fasta)
[2023-03-15 21:03:34,757] [INFO] Task started: Blastn
[2023-03-15 21:03:34,757] [INFO] Running command: blastn -query OceanDNA-b30/markers.fasta -db /var/lib/cwl/stg3529c246-c97f-4d88-af50-5ec91e3cc687/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:35,560] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:35,561] [INFO] Selected 20 target genomes.
[2023-03-15 21:03:35,561] [INFO] Target genome list was writen to OceanDNA-b30/target_genomes_gtdb.txt
[2023-03-15 21:03:36,147] [INFO] Task started: fastANI
[2023-03-15 21:03:36,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7230a1-9be3-4ccd-b1a1-878ca1769606/OceanDNA-b30.fa --refList OceanDNA-b30/target_genomes_gtdb.txt --output OceanDNA-b30/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:51,341] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:51,343] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:51,344] [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_009838515.1	s__VXMF01 sp009838515	75.2101	60	1565	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__VXMF01	95.0	99.95	99.93	0.99	0.98	3	-
GCA_018268835.1	s__Solibacter sp018268835	75.0691	60	1565	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:51,344] [INFO] GTDB search result was written to OceanDNA-b30/result_gtdb.tsv
[2023-03-15 21:03:51,344] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:51,344] [INFO] DFAST_QC result json was written to OceanDNA-b30/dqc_result.json
[2023-03-15 21:03:51,345] [INFO] DFAST_QC completed!
[2023-03-15 21:03:51,345] [INFO] Total running time: 0h2m7s