[2024-01-24 10:47:40,973] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg146ff333-f978-4da9-a86a-5cc9163c3c13/GCF_013387005.1_ASM1338700v1_genomic.fna.gz | prodigal -d GCF_013387005.1_ASM1338700v1_genomic.fna/cds.fna -a GCF_013387005.1_ASM1338700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:05,464] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:05,465] [INFO] Task started: HMMsearch
[2024-01-24 10:48:05,465] [INFO] Running command: hmmsearch --tblout GCF_013387005.1_ASM1338700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/reference_markers.hmm GCF_013387005.1_ASM1338700v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:05,797] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:05,799] [INFO] Found 6/6 markers.
[2024-01-24 10:48:05,851] [INFO] Query marker FASTA was written to GCF_013387005.1_ASM1338700v1_genomic.fna/markers.fasta
[2024-01-24 10:48:05,851] [INFO] Task started: Blastn
[2024-01-24 10:48:05,851] [INFO] Running command: blastn -query GCF_013387005.1_ASM1338700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/reference_markers.fasta -out GCF_013387005.1_ASM1338700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:06,849] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:06,852] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:06,852] [INFO] Target genome list was writen to GCF_013387005.1_ASM1338700v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:06,857] [INFO] Task started: fastANI
[2024-01-24 10:48:06,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg146ff333-f978-4da9-a86a-5cc9163c3c13/GCF_013387005.1_ASM1338700v1_genomic.fna.gz --refList GCF_013387005.1_ASM1338700v1_genomic.fna/target_genomes.txt --output GCF_013387005.1_ASM1338700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:26,530] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:26,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:26,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:26,549] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:48:26,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:26,550] [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=IPO3752	GCA_013387005.1	303	303	suspected-type	True	100.0	1989	1995	95	conclusive
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	99.9939	1994	1995	95	conclusive
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	99.9938	1994	1995	95	conclusive
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	99.9883	1989	1995	95	conclusive
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	90.6064	1525	1995	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	90.0876	1502	1995	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.8154	1361	1995	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.7566	1445	1995	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.7555	1388	1995	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.6682	1548	1995	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.2361	1430	1995	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	85.8352	1255	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,551] [INFO] DFAST Taxonomy check result was written to GCF_013387005.1_ASM1338700v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:26,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:26,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:26,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/checkm_data
[2024-01-24 10:48:26,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:26,620] [INFO] Task started: CheckM
[2024-01-24 10:48:26,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013387005.1_ASM1338700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013387005.1_ASM1338700v1_genomic.fna/checkm_input GCF_013387005.1_ASM1338700v1_genomic.fna/checkm_result
[2024-01-24 10:49:24,873] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:24,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:24,893] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:24,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:24,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013387005.1_ASM1338700v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:24,894] [INFO] Task started: Blastn
[2024-01-24 10:49:24,894] [INFO] Running command: blastn -query GCF_013387005.1_ASM1338700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05d23472-2173-47c6-b2af-1ade9a4ddf49/dqc_reference/reference_markers_gtdb.fasta -out GCF_013387005.1_ASM1338700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:26,756] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:26,759] [INFO] Selected 12 target genomes.
[2024-01-24 10:49:26,759] [INFO] Target genome list was writen to GCF_013387005.1_ASM1338700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:26,783] [INFO] Task started: fastANI
[2024-01-24 10:49:26,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg146ff333-f978-4da9-a86a-5cc9163c3c13/GCF_013387005.1_ASM1338700v1_genomic.fna.gz --refList GCF_013387005.1_ASM1338700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013387005.1_ASM1338700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:47,246] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:47,263] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:47,263] [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	99.9939	1994	1995	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	94.9394	1753	1995	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	94.8057	1684	1995	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	94.0864	1711	1995	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	90.7709	1621	1995	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	90.5206	1504	1995	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	90.0789	1503	1995	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	90.0682	1563	1995	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	89.1706	1399	1995	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_000731675.1	s__Pseudomonas_E capeferrum	87.6744	1548	1995	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_002736125.1	s__Pseudomonas_E putida_M	87.6492	1570	1995	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_000282535.1	s__Pseudomonas_E sp000282535	87.2082	1300	1995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:47,266] [INFO] GTDB search result was written to GCF_013387005.1_ASM1338700v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:47,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:47,270] [INFO] DFAST_QC result json was written to GCF_013387005.1_ASM1338700v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:47,271] [INFO] DFAST_QC completed!
[2024-01-24 10:49:47,271] [INFO] Total running time: 0h2m6s