[2023-03-18 23:11:06,985] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference
[2023-03-18 23:11:08,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,359] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,359] [INFO] Running command: cat /var/lib/cwl/stgd1f4d05a-0aa4-4e55-8bca-7ca084cd9306/OceanDNA-b16189.fa | prodigal -d OceanDNA-b16189/cds.fna -a OceanDNA-b16189/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:12:09,520] [INFO] Task succeeded: Prodigal
[2023-03-18 23:12:09,520] [INFO] Task started: HMMsearch
[2023-03-18 23:12:09,520] [INFO] Running command: hmmsearch --tblout OceanDNA-b16189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/reference_markers.hmm OceanDNA-b16189/protein.faa > /dev/null
[2023-03-18 23:12:09,923] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:12:09,923] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd1f4d05a-0aa4-4e55-8bca-7ca084cd9306/OceanDNA-b16189.fa]
[2023-03-18 23:12:09,979] [INFO] Query marker FASTA was written to OceanDNA-b16189/markers.fasta
[2023-03-18 23:12:09,980] [INFO] Task started: Blastn
[2023-03-18 23:12:09,980] [INFO] Running command: blastn -query OceanDNA-b16189/markers.fasta -db /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/reference_markers.fasta -out OceanDNA-b16189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:13,543] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:13,544] [INFO] Selected 21 target genomes.
[2023-03-18 23:12:13,544] [INFO] Target genome list was writen to OceanDNA-b16189/target_genomes.txt
[2023-03-18 23:12:13,555] [INFO] Task started: fastANI
[2023-03-18 23:12:13,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f4d05a-0aa4-4e55-8bca-7ca084cd9306/OceanDNA-b16189.fa --refList OceanDNA-b16189/target_genomes.txt --output OceanDNA-b16189/fastani_result.tsv --threads 1
[2023-03-18 23:12:25,561] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:25,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:12:25,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:12:25,565] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:12:25,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:12:25,565] [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
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	75.2192	66	3379	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	75.1385	69	3379	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:12:25,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16189/tc_result.tsv
[2023-03-18 23:12:25,566] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:12:25,566] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:12:25,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/checkm_data
[2023-03-18 23:12:25,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:12:25,603] [INFO] Task started: CheckM
[2023-03-18 23:12:25,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16189/checkm_input OceanDNA-b16189/checkm_result
[2023-03-18 23:14:49,277] [INFO] Task succeeded: CheckM
[2023-03-18 23:14:49,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:14:49,283] [INFO] ===== Completeness check finished =====
[2023-03-18 23:14:49,283] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:14:49,283] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16189/markers.fasta)
[2023-03-18 23:14:49,284] [INFO] Task started: Blastn
[2023-03-18 23:14:49,284] [INFO] Running command: blastn -query OceanDNA-b16189/markers.fasta -db /var/lib/cwl/stg154a9ef6-6e24-47c7-a72e-9bb0b7f5f617/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:14:49,978] [INFO] Task succeeded: Blastn
[2023-03-18 23:14:49,979] [INFO] Selected 29 target genomes.
[2023-03-18 23:14:49,979] [INFO] Target genome list was writen to OceanDNA-b16189/target_genomes_gtdb.txt
[2023-03-18 23:14:50,004] [INFO] Task started: fastANI
[2023-03-18 23:14:50,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f4d05a-0aa4-4e55-8bca-7ca084cd9306/OceanDNA-b16189.fa --refList OceanDNA-b16189/target_genomes_gtdb.txt --output OceanDNA-b16189/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:15:13,206] [INFO] Task succeeded: fastANI
[2023-03-18 23:15:13,214] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:15:13,214] [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_012031415.1	s__JAAUTN01 sp012031415	75.5249	91	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTN01	95.0	99.26	99.26	0.85	0.85	2	-
GCA_010692325.1	s__Moorea sp010692325	75.4176	64	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCA_000733415.1	s__Elainella sp000733415	75.3149	73	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Elainella	95.0	96.63	96.48	0.89	0.88	3	-
GCF_014695915.1	s__FACHB-40 sp014695915	75.2675	72	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__FACHB-T130;g__FACHB-40	95.0	96.30	95.91	0.87	0.85	6	-
GCF_000763385.1	s__Nodosilinea sp000763385	75.2304	61	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208305.1	s__JAAUOQ01 sp016208305	75.2283	54	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003017855.1	s__Nodosilinea sp003017855	75.2154	65	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_017164015.1	s__Amazonocrinis sp017164015	75.1801	61	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016743235.1	s__Pantanalinema sp016743235	75.1623	63	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249025.1	s__ULC077BIN1 sp003249025	75.0839	55	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692425.1	s__SIO3C6 sp010692425	75.0535	73	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO3C6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207735.1	s__Phormidium_B sp015207735	74.8941	67	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__Phormidium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022385.1	s__Nodosilinea sp003022385	74.8431	59	3379	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:15:13,214] [INFO] GTDB search result was written to OceanDNA-b16189/result_gtdb.tsv
[2023-03-18 23:15:13,214] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:15:13,215] [INFO] DFAST_QC result json was written to OceanDNA-b16189/dqc_result.json
[2023-03-18 23:15:13,215] [INFO] DFAST_QC completed!
[2023-03-18 23:15:13,215] [INFO] Total running time: 0h4m6s