[2024-01-25 19:49:05,548] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:05,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:05,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference
[2024-01-25 19:49:06,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:06,739] [INFO] Task started: Prodigal
[2024-01-25 19:49:06,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b12335-1a03-47d8-830f-9562eb5c3eb4/GCF_900455645.1_43222_D01_genomic.fna.gz | prodigal -d GCF_900455645.1_43222_D01_genomic.fna/cds.fna -a GCF_900455645.1_43222_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:30,941] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:30,941] [INFO] Task started: HMMsearch
[2024-01-25 19:49:30,942] [INFO] Running command: hmmsearch --tblout GCF_900455645.1_43222_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/reference_markers.hmm GCF_900455645.1_43222_D01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:31,237] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:31,238] [INFO] Found 6/6 markers.
[2024-01-25 19:49:31,296] [INFO] Query marker FASTA was written to GCF_900455645.1_43222_D01_genomic.fna/markers.fasta
[2024-01-25 19:49:31,298] [INFO] Task started: Blastn
[2024-01-25 19:49:31,298] [INFO] Running command: blastn -query GCF_900455645.1_43222_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/reference_markers.fasta -out GCF_900455645.1_43222_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:32,290] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:32,293] [INFO] Selected 12 target genomes.
[2024-01-25 19:49:32,293] [INFO] Target genome list was writen to GCF_900455645.1_43222_D01_genomic.fna/target_genomes.txt
[2024-01-25 19:49:32,299] [INFO] Task started: fastANI
[2024-01-25 19:49:32,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b12335-1a03-47d8-830f-9562eb5c3eb4/GCF_900455645.1_43222_D01_genomic.fna.gz --refList GCF_900455645.1_43222_D01_genomic.fna/target_genomes.txt --output GCF_900455645.1_43222_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:52,360] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:52,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:52,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:52,369] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:49:52,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:52,369] [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
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	100.0	2044	2045	95	conclusive
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	99.9933	2043	2045	95	conclusive
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	99.9919	2043	2045	95	conclusive
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	99.9675	1984	2045	95	conclusive
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	90.5202	1565	2045	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	90.1111	1541	2045	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.7584	1406	2045	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.7478	1561	2045	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.7454	1382	2045	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.7096	1474	2045	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.3167	1432	2045	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	85.8149	1276	2045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:52,372] [INFO] DFAST Taxonomy check result was written to GCF_900455645.1_43222_D01_genomic.fna/tc_result.tsv
[2024-01-25 19:49:52,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:52,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:52,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/checkm_data
[2024-01-25 19:49:52,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:52,435] [INFO] Task started: CheckM
[2024-01-25 19:49:52,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455645.1_43222_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455645.1_43222_D01_genomic.fna/checkm_input GCF_900455645.1_43222_D01_genomic.fna/checkm_result
[2024-01-25 19:51:02,956] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:02,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:02,974] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:02,974] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:02,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455645.1_43222_D01_genomic.fna/markers.fasta)
[2024-01-25 19:51:02,975] [INFO] Task started: Blastn
[2024-01-25 19:51:02,976] [INFO] Running command: blastn -query GCF_900455645.1_43222_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgacec68c4-aaac-45b0-b7b6-8030979885ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455645.1_43222_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:04,827] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:04,830] [INFO] Selected 12 target genomes.
[2024-01-25 19:51:04,830] [INFO] Target genome list was writen to GCF_900455645.1_43222_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:04,861] [INFO] Task started: fastANI
[2024-01-25 19:51:04,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b12335-1a03-47d8-830f-9562eb5c3eb4/GCF_900455645.1_43222_D01_genomic.fna.gz --refList GCF_900455645.1_43222_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900455645.1_43222_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:26,205] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:26,214] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:26,214] [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
GCF_000412675.1	s__Pseudomonas_E putida	99.9919	2043	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	conclusive
GCF_000498395.2	s__Pseudomonas_E putida_Q	94.9142	1787	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	97.78	0.93	0.90	5	-
GCF_000708715.2	s__Pseudomonas_E putida_R	94.6918	1724	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_002356095.1	s__Pseudomonas_E putida_H	94.1545	1727	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
GCF_013393325.1	s__Pseudomonas_E putida_P	90.7517	1653	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	90.4936	1538	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_900277125.1	s__Pseudomonas_E inefficax	90.1056	1542	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	90.0842	1583	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	89.216	1413	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_002736125.1	s__Pseudomonas_E putida_M	87.7883	1598	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	87.7555	1559	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	87.3028	1314	2045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:26,215] [INFO] GTDB search result was written to GCF_900455645.1_43222_D01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:26,216] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:26,219] [INFO] DFAST_QC result json was written to GCF_900455645.1_43222_D01_genomic.fna/dqc_result.json
[2024-01-25 19:51:26,219] [INFO] DFAST_QC completed!
[2024-01-25 19:51:26,219] [INFO] Total running time: 0h2m21s