[2023-03-15 03:48:48,725] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:48:48,725] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:48:48,725] [INFO] DQC Reference Directory: /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference
[2023-03-15 03:48:49,846] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:48:49,846] [INFO] Task started: Prodigal
[2023-03-15 03:48:49,846] [INFO] Running command: cat /var/lib/cwl/stgc8a169fd-5a79-4416-af23-2d05d5920b71/OceanDNA-b289.fa | prodigal -d OceanDNA-b289/cds.fna -a OceanDNA-b289/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:49:08,773] [INFO] Task succeeded: Prodigal
[2023-03-15 03:49:08,773] [INFO] Task started: HMMsearch
[2023-03-15 03:49:08,773] [INFO] Running command: hmmsearch --tblout OceanDNA-b289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/reference_markers.hmm OceanDNA-b289/protein.faa > /dev/null
[2023-03-15 03:49:08,976] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:49:08,977] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8a169fd-5a79-4416-af23-2d05d5920b71/OceanDNA-b289.fa]
[2023-03-15 03:49:09,006] [INFO] Query marker FASTA was written to OceanDNA-b289/markers.fasta
[2023-03-15 03:49:09,007] [INFO] Task started: Blastn
[2023-03-15 03:49:09,007] [INFO] Running command: blastn -query OceanDNA-b289/markers.fasta -db /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/reference_markers.fasta -out OceanDNA-b289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:49:09,598] [INFO] Task succeeded: Blastn
[2023-03-15 03:49:09,599] [INFO] Selected 24 target genomes.
[2023-03-15 03:49:09,599] [INFO] Target genome list was writen to OceanDNA-b289/target_genomes.txt
[2023-03-15 03:49:09,612] [INFO] Task started: fastANI
[2023-03-15 03:49:09,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a169fd-5a79-4416-af23-2d05d5920b71/OceanDNA-b289.fa --refList OceanDNA-b289/target_genomes.txt --output OceanDNA-b289/fastani_result.tsv --threads 1
[2023-03-15 03:49:30,303] [INFO] Task succeeded: fastANI
[2023-03-15 03:49:30,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:49:30,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:49:30,307] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:49:30,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:49:30,307] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.7944	62	909	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:49:30,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b289/tc_result.tsv
[2023-03-15 03:49:30,307] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:49:30,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:49:30,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/checkm_data
[2023-03-15 03:49:30,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:49:30,314] [INFO] Task started: CheckM
[2023-03-15 03:49:30,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b289/checkm_input OceanDNA-b289/checkm_result
[2023-03-15 03:50:18,774] [INFO] Task succeeded: CheckM
[2023-03-15 03:50:18,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:50:18,778] [INFO] ===== Completeness check finished =====
[2023-03-15 03:50:18,778] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:50:18,778] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b289/markers.fasta)
[2023-03-15 03:50:18,779] [INFO] Task started: Blastn
[2023-03-15 03:50:18,780] [INFO] Running command: blastn -query OceanDNA-b289/markers.fasta -db /var/lib/cwl/stgf05f5276-21e4-4e74-8fa5-cb0c2bc0a6d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:50:19,770] [INFO] Task succeeded: Blastn
[2023-03-15 03:50:19,771] [INFO] Selected 16 target genomes.
[2023-03-15 03:50:19,771] [INFO] Target genome list was writen to OceanDNA-b289/target_genomes_gtdb.txt
[2023-03-15 03:50:19,785] [INFO] Task started: fastANI
[2023-03-15 03:50:19,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8a169fd-5a79-4416-af23-2d05d5920b71/OceanDNA-b289.fa --refList OceanDNA-b289/target_genomes_gtdb.txt --output OceanDNA-b289/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:50:31,569] [INFO] Task succeeded: fastANI
[2023-03-15 03:50:31,577] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:50:31,577] [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_002712885.1	s__UBA8438 sp002712885	81.7602	499	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	78.5033	320	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	77.4749	226	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	77.2523	262	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	76.6143	143	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_011523845.1	s__WTFV01 sp011523845	76.3447	162	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.329	68	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_002730525.1	s__UBA2161 sp002730525	76.2406	67	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871255.1	s__VFZH01 sp016871255	75.5164	69	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	75.3908	56	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_016865485.1	s__Luteitalea sp016865485	75.2089	67	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	75.1415	58	909	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:50:31,577] [INFO] GTDB search result was written to OceanDNA-b289/result_gtdb.tsv
[2023-03-15 03:50:31,577] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:50:31,578] [INFO] DFAST_QC result json was written to OceanDNA-b289/dqc_result.json
[2023-03-15 03:50:31,579] [INFO] DFAST_QC completed!
[2023-03-15 03:50:31,579] [INFO] Total running time: 0h1m43s