[2023-03-17 03:16:27,138] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:16:27,138] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:16:27,138] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference
[2023-03-17 03:16:29,892] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:16:29,893] [INFO] Task started: Prodigal
[2023-03-17 03:16:29,893] [INFO] Running command: cat /var/lib/cwl/stgaa9f7edf-8f9e-4972-9b33-fe0a217e0228/OceanDNA-b16232.fa | prodigal -d OceanDNA-b16232/cds.fna -a OceanDNA-b16232/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:16:58,869] [INFO] Task succeeded: Prodigal
[2023-03-17 03:16:58,870] [INFO] Task started: HMMsearch
[2023-03-17 03:16:58,870] [INFO] Running command: hmmsearch --tblout OceanDNA-b16232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/reference_markers.hmm OceanDNA-b16232/protein.faa > /dev/null
[2023-03-17 03:16:59,117] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:16:59,118] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaa9f7edf-8f9e-4972-9b33-fe0a217e0228/OceanDNA-b16232.fa]
[2023-03-17 03:16:59,148] [INFO] Query marker FASTA was written to OceanDNA-b16232/markers.fasta
[2023-03-17 03:16:59,149] [INFO] Task started: Blastn
[2023-03-17 03:16:59,149] [INFO] Running command: blastn -query OceanDNA-b16232/markers.fasta -db /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/reference_markers.fasta -out OceanDNA-b16232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:16:59,665] [INFO] Task succeeded: Blastn
[2023-03-17 03:16:59,666] [INFO] Selected 25 target genomes.
[2023-03-17 03:16:59,666] [INFO] Target genome list was writen to OceanDNA-b16232/target_genomes.txt
[2023-03-17 03:16:59,741] [INFO] Task started: fastANI
[2023-03-17 03:16:59,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9f7edf-8f9e-4972-9b33-fe0a217e0228/OceanDNA-b16232.fa --refList OceanDNA-b16232/target_genomes.txt --output OceanDNA-b16232/fastani_result.tsv --threads 1
[2023-03-17 03:17:18,526] [INFO] Task succeeded: fastANI
[2023-03-17 03:17:18,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:17:18,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:17:18,530] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:17:18,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:17:18,530] [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
Adonisia turfae	strain=CCMR0081	GCA_011009555.1	2950184	2950184	type	True	75.603	73	1728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:17:18,530] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16232/tc_result.tsv
[2023-03-17 03:17:18,531] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:17:18,531] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:17:18,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/checkm_data
[2023-03-17 03:17:18,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:17:18,611] [INFO] Task started: CheckM
[2023-03-17 03:17:18,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16232/checkm_input OceanDNA-b16232/checkm_result
[2023-03-17 03:18:28,701] [INFO] Task succeeded: CheckM
[2023-03-17 03:18:28,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:18:28,705] [INFO] ===== Completeness check finished =====
[2023-03-17 03:18:28,705] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:18:28,705] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16232/markers.fasta)
[2023-03-17 03:18:28,706] [INFO] Task started: Blastn
[2023-03-17 03:18:28,706] [INFO] Running command: blastn -query OceanDNA-b16232/markers.fasta -db /var/lib/cwl/stgf5f2c8f5-da35-40b0-b68f-253471782a29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:18:29,418] [INFO] Task succeeded: Blastn
[2023-03-17 03:18:29,420] [INFO] Selected 22 target genomes.
[2023-03-17 03:18:29,420] [INFO] Target genome list was writen to OceanDNA-b16232/target_genomes_gtdb.txt
[2023-03-17 03:18:29,537] [INFO] Task started: fastANI
[2023-03-17 03:18:29,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9f7edf-8f9e-4972-9b33-fe0a217e0228/OceanDNA-b16232.fa --refList OceanDNA-b16232/target_genomes_gtdb.txt --output OceanDNA-b16232/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:18:46,667] [INFO] Task succeeded: fastANI
[2023-03-17 03:18:46,675] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:18:46,675] [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_015207105.1	s__Phormidesmis sp015207105	77.622	393	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242035.1	s__Phormidesmis foveolarum	77.0139	335	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286735.1	s__Phormidesmis sp002286735	77.0125	398	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242115.1	s__Phormidesmis priestleyi_A	76.9956	365	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314865.1	s__Phormidesmis priestleyi_B	76.9557	388	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033015.1	s__Phormidesmis sp012033015	76.9185	287	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155595.1	s__Phormidesmis sp000155595	76.6516	294	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316115.1	s__Leptothoe sp000316115	75.8333	77	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241845.1	s__Nodosilinea antarctica	75.7258	84	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
GCA_011009555.1	s__Leptothoe sp011009555	75.603	73	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Leptothoe	95.0	98.38	98.38	0.89	0.89	2	-
GCF_000309385.1	s__Nodosilinea nodulosa	75.5098	82	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671975.1	s__SIO4C1 sp010671975	75.4275	110	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO4C1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272155.1	s__JACYME01 sp015272155	75.4014	63	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACYME01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695775.1	s__Nodosilinea sp014695775	75.3596	86	1728	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-17 03:18:46,676] [INFO] GTDB search result was written to OceanDNA-b16232/result_gtdb.tsv
[2023-03-17 03:18:46,676] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:18:46,678] [INFO] DFAST_QC result json was written to OceanDNA-b16232/dqc_result.json
[2023-03-17 03:18:46,678] [INFO] DFAST_QC completed!
[2023-03-17 03:18:46,678] [INFO] Total running time: 0h2m20s