[2023-03-14 12:38:54,610] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:38:54,610] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:38:54,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference
[2023-03-14 12:38:57,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:38:57,151] [INFO] Task started: Prodigal
[2023-03-14 12:38:57,152] [INFO] Running command: cat /var/lib/cwl/stg7e1769ad-564e-4647-951c-bd17b2013e2d/OceanDNA-b109.fa | prodigal -d OceanDNA-b109/cds.fna -a OceanDNA-b109/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:39:22,915] [INFO] Task succeeded: Prodigal
[2023-03-14 12:39:22,915] [INFO] Task started: HMMsearch
[2023-03-14 12:39:22,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b109/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/reference_markers.hmm OceanDNA-b109/protein.faa > /dev/null
[2023-03-14 12:39:23,129] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:39:23,129] [INFO] Found 6/6 markers.
[2023-03-14 12:39:23,158] [INFO] Query marker FASTA was written to OceanDNA-b109/markers.fasta
[2023-03-14 12:39:23,160] [INFO] Task started: Blastn
[2023-03-14 12:39:23,160] [INFO] Running command: blastn -query OceanDNA-b109/markers.fasta -db /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/reference_markers.fasta -out OceanDNA-b109/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:39:23,711] [INFO] Task succeeded: Blastn
[2023-03-14 12:39:23,713] [INFO] Selected 29 target genomes.
[2023-03-14 12:39:23,714] [INFO] Target genome list was writen to OceanDNA-b109/target_genomes.txt
[2023-03-14 12:39:23,731] [INFO] Task started: fastANI
[2023-03-14 12:39:23,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1769ad-564e-4647-951c-bd17b2013e2d/OceanDNA-b109.fa --refList OceanDNA-b109/target_genomes.txt --output OceanDNA-b109/fastani_result.tsv --threads 1
[2023-03-14 12:39:51,766] [INFO] Task succeeded: fastANI
[2023-03-14 12:39:51,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:39:51,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:39:51,771] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:39:51,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:39:51,772] [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	75.8425	68	1102	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:39:51,774] [INFO] DFAST Taxonomy check result was written to OceanDNA-b109/tc_result.tsv
[2023-03-14 12:39:51,774] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:39:51,774] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:39:51,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/checkm_data
[2023-03-14 12:39:51,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:39:51,782] [INFO] Task started: CheckM
[2023-03-14 12:39:51,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b109/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b109/checkm_input OceanDNA-b109/checkm_result
[2023-03-14 12:40:54,166] [INFO] Task succeeded: CheckM
[2023-03-14 12:40:54,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:40:54,170] [INFO] ===== Completeness check finished =====
[2023-03-14 12:40:54,171] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:40:54,171] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b109/markers.fasta)
[2023-03-14 12:40:54,173] [INFO] Task started: Blastn
[2023-03-14 12:40:54,173] [INFO] Running command: blastn -query OceanDNA-b109/markers.fasta -db /var/lib/cwl/stgec20e51a-c487-449c-8301-4837e0487176/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b109/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:40:55,040] [INFO] Task succeeded: Blastn
[2023-03-14 12:40:55,041] [INFO] Selected 13 target genomes.
[2023-03-14 12:40:55,042] [INFO] Target genome list was writen to OceanDNA-b109/target_genomes_gtdb.txt
[2023-03-14 12:40:55,079] [INFO] Task started: fastANI
[2023-03-14 12:40:55,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1769ad-564e-4647-951c-bd17b2013e2d/OceanDNA-b109.fa --refList OceanDNA-b109/target_genomes_gtdb.txt --output OceanDNA-b109/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:41:05,297] [INFO] Task succeeded: fastANI
[2023-03-14 12:41:05,304] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:41:05,305] [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_013203475.1	s__SYFT01 sp013203475	99.3925	912	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SYFT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016716905.1	s__SYFT01 sp016716905	77.4483	336	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694745.1	s__SYFT01 sp009694745	77.445	235	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005799825.1	s__SYFT01 sp005799825	77.1958	215	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SYFT01	95.0	99.95	99.95	0.96	0.95	4	-
GCA_016871335.1	s__SYFT01 sp016871335	77.118	208	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242705.1	s__SCN-69-37 sp003242705	76.3432	87	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SCN-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694735.1	s__12-FULL-67-14b sp009694735	76.2735	58	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737365.1	s__12-FULL-67-14b sp002737365	76.2436	76	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	97.27	96.58	0.83	0.80	6	-
GCA_001767435.1	s__2-02-FULL-65-29 sp001767435	75.7977	64	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__2-02-FULL-65-29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	75.6656	86	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	75.5814	69	1102	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:41:05,305] [INFO] GTDB search result was written to OceanDNA-b109/result_gtdb.tsv
[2023-03-14 12:41:05,305] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:41:05,306] [INFO] DFAST_QC result json was written to OceanDNA-b109/dqc_result.json
[2023-03-14 12:41:05,306] [INFO] DFAST_QC completed!
[2023-03-14 12:41:05,307] [INFO] Total running time: 0h2m11s