[2023-03-17 04:48:53,954] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,955] [INFO] DQC Reference Directory: /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference
[2023-03-17 04:48:55,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,156] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,156] [INFO] Running command: cat /var/lib/cwl/stgf661d480-55df-4016-9c35-ca16a5e564b5/OceanDNA-b27632.fa | prodigal -d OceanDNA-b27632/cds.fna -a OceanDNA-b27632/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:11,641] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:11,642] [INFO] Task started: HMMsearch
[2023-03-17 04:49:11,642] [INFO] Running command: hmmsearch --tblout OceanDNA-b27632/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/reference_markers.hmm OceanDNA-b27632/protein.faa > /dev/null
[2023-03-17 04:49:11,814] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:11,815] [INFO] Found 6/6 markers.
[2023-03-17 04:49:11,831] [INFO] Query marker FASTA was written to OceanDNA-b27632/markers.fasta
[2023-03-17 04:49:11,831] [INFO] Task started: Blastn
[2023-03-17 04:49:11,831] [INFO] Running command: blastn -query OceanDNA-b27632/markers.fasta -db /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/reference_markers.fasta -out OceanDNA-b27632/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:12,435] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:12,436] [INFO] Selected 30 target genomes.
[2023-03-17 04:49:12,436] [INFO] Target genome list was writen to OceanDNA-b27632/target_genomes.txt
[2023-03-17 04:49:12,451] [INFO] Task started: fastANI
[2023-03-17 04:49:12,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgf661d480-55df-4016-9c35-ca16a5e564b5/OceanDNA-b27632.fa --refList OceanDNA-b27632/target_genomes.txt --output OceanDNA-b27632/fastani_result.tsv --threads 1
[2023-03-17 04:49:28,851] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:28,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:28,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:28,856] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:28,856] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:49:28,856] [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
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	77.0945	176	826	95	below_threshold
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	76.7351	189	826	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	75.6058	50	826	95	below_threshold
Pacificibacter marinus	strain=DSM 25228	GCA_900109555.1	658057	658057	type	True	75.4846	50	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:49:28,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27632/tc_result.tsv
[2023-03-17 04:49:28,856] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:28,856] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:28,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/checkm_data
[2023-03-17 04:49:28,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:28,861] [INFO] Task started: CheckM
[2023-03-17 04:49:28,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27632/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27632/checkm_input OceanDNA-b27632/checkm_result
[2023-03-17 04:50:13,107] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:13,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:13,494] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:13,494] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:13,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27632/markers.fasta)
[2023-03-17 04:50:13,495] [INFO] Task started: Blastn
[2023-03-17 04:50:13,495] [INFO] Running command: blastn -query OceanDNA-b27632/markers.fasta -db /var/lib/cwl/stgc870c22e-4185-4df8-a61f-306505cdfa61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27632/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:14,520] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:14,521] [INFO] Selected 27 target genomes.
[2023-03-17 04:50:14,521] [INFO] Target genome list was writen to OceanDNA-b27632/target_genomes_gtdb.txt
[2023-03-17 04:50:15,052] [INFO] Task started: fastANI
[2023-03-17 04:50:15,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgf661d480-55df-4016-9c35-ca16a5e564b5/OceanDNA-b27632.fa --refList OceanDNA-b27632/target_genomes_gtdb.txt --output OceanDNA-b27632/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:29,377] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:29,383] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:50:29,383] [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_002469545.1	s__Amylibacter sp002469545	79.6308	277	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181935.1	s__Amylibacter sp905181935	77.3573	87	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153745.1	s__Amylibacter sp000153745	77.2013	56	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	98.38	97.19	0.95	0.89	11	-
GCF_014652655.1	s__Amylibacter ulvae	77.0945	176	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742285.1	s__Amylibacter kogurei	76.7351	189	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401045.1	s__Amylibacter sp002401045	76.5708	57	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764475.1	s__Amylibacter sp016764475	76.2798	87	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860325.1	s__Amylibacter lutimaris	75.8272	52	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643735.1	s__Amylibacter cionae	75.6618	65	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:29,384] [INFO] GTDB search result was written to OceanDNA-b27632/result_gtdb.tsv
[2023-03-17 04:50:29,384] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:29,385] [INFO] DFAST_QC result json was written to OceanDNA-b27632/dqc_result.json
[2023-03-17 04:50:29,385] [INFO] DFAST_QC completed!
[2023-03-17 04:50:29,385] [INFO] Total running time: 0h1m35s