[2023-03-17 11:36:53,966] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:53,966] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:53,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference
[2023-03-17 11:36:55,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,181] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,182] [INFO] Running command: cat /var/lib/cwl/stg0b03c82e-2abb-48f7-ae26-5284e9a52f7f/OceanDNA-b16112.fa | prodigal -d OceanDNA-b16112/cds.fna -a OceanDNA-b16112/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:37:01,410] [INFO] Task succeeded: Prodigal
[2023-03-17 11:37:01,411] [INFO] Task started: HMMsearch
[2023-03-17 11:37:01,411] [INFO] Running command: hmmsearch --tblout OceanDNA-b16112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/reference_markers.hmm OceanDNA-b16112/protein.faa > /dev/null
[2023-03-17 11:37:01,577] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:37:01,577] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b03c82e-2abb-48f7-ae26-5284e9a52f7f/OceanDNA-b16112.fa]
[2023-03-17 11:37:01,600] [INFO] Query marker FASTA was written to OceanDNA-b16112/markers.fasta
[2023-03-17 11:37:01,602] [INFO] Task started: Blastn
[2023-03-17 11:37:01,602] [INFO] Running command: blastn -query OceanDNA-b16112/markers.fasta -db /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/reference_markers.fasta -out OceanDNA-b16112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:02,042] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:02,044] [INFO] Selected 11 target genomes.
[2023-03-17 11:37:02,045] [INFO] Target genome list was writen to OceanDNA-b16112/target_genomes.txt
[2023-03-17 11:37:02,052] [INFO] Task started: fastANI
[2023-03-17 11:37:02,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b03c82e-2abb-48f7-ae26-5284e9a52f7f/OceanDNA-b16112.fa --refList OceanDNA-b16112/target_genomes.txt --output OceanDNA-b16112/fastani_result.tsv --threads 1
[2023-03-17 11:37:09,698] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:09,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:09,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:09,702] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:09,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:37:09,702] [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
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	81.2069	75	100	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:37:09,704] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16112/tc_result.tsv
[2023-03-17 11:37:09,704] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:09,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:09,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/checkm_data
[2023-03-17 11:37:09,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:09,808] [INFO] Task started: CheckM
[2023-03-17 11:37:09,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16112/checkm_input OceanDNA-b16112/checkm_result
[2023-03-17 11:37:31,823] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:31,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.30%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:37:31,844] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:31,844] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:31,844] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16112/markers.fasta)
[2023-03-17 11:37:31,845] [INFO] Task started: Blastn
[2023-03-17 11:37:31,845] [INFO] Running command: blastn -query OceanDNA-b16112/markers.fasta -db /var/lib/cwl/stg92c1f2cf-1a5a-4a5f-8f4d-6b02194f3bc4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:32,268] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:32,271] [INFO] Selected 7 target genomes.
[2023-03-17 11:37:32,271] [INFO] Target genome list was writen to OceanDNA-b16112/target_genomes_gtdb.txt
[2023-03-17 11:37:32,277] [INFO] Task started: fastANI
[2023-03-17 11:37:32,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b03c82e-2abb-48f7-ae26-5284e9a52f7f/OceanDNA-b16112.fa --refList OceanDNA-b16112/target_genomes_gtdb.txt --output OceanDNA-b16112/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:37:41,046] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:41,051] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:37:41,051] [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
GCF_000014265.1	s__Trichodesmium erythraeum	87.981	92	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	99.96	99.96	0.99	0.99	2	-
GCA_010672085.1	s__Trichodesmium sp010672085	84.4662	79	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672455.1	s__Okeania sp010672455	82.1039	75	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672525.1	s__Okeania sp010672525	81.3441	73	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672585.1	s__Okeania sp010672585	81.3273	75	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003838195.1	s__Okeania hirsuta	81.2069	75	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	98.05	95.33	0.88	0.84	10	-
GCA_010692555.1	s__Okeania sp010692555	81.0062	81	100	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:37:41,052] [INFO] GTDB search result was written to OceanDNA-b16112/result_gtdb.tsv
[2023-03-17 11:37:41,052] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:37:41,053] [INFO] DFAST_QC result json was written to OceanDNA-b16112/dqc_result.json
[2023-03-17 11:37:41,053] [INFO] DFAST_QC completed!
[2023-03-17 11:37:41,053] [INFO] Total running time: 0h0m47s