[2024-01-24 14:20:16,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:16,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:16,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference
[2024-01-24 14:20:17,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:17,796] [INFO] Task started: Prodigal
[2024-01-24 14:20:17,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8b7e8c8-f057-4836-b156-7ff07905d9ef/GCF_002091535.1_ASM209153v1_genomic.fna.gz | prodigal -d GCF_002091535.1_ASM209153v1_genomic.fna/cds.fna -a GCF_002091535.1_ASM209153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:40,931] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:40,932] [INFO] Task started: HMMsearch
[2024-01-24 14:20:40,932] [INFO] Running command: hmmsearch --tblout GCF_002091535.1_ASM209153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/reference_markers.hmm GCF_002091535.1_ASM209153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:41,280] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:41,282] [INFO] Found 6/6 markers.
[2024-01-24 14:20:41,340] [INFO] Query marker FASTA was written to GCF_002091535.1_ASM209153v1_genomic.fna/markers.fasta
[2024-01-24 14:20:41,340] [INFO] Task started: Blastn
[2024-01-24 14:20:41,341] [INFO] Running command: blastn -query GCF_002091535.1_ASM209153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/reference_markers.fasta -out GCF_002091535.1_ASM209153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:42,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:42,326] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:42,327] [INFO] Target genome list was writen to GCF_002091535.1_ASM209153v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:42,332] [INFO] Task started: fastANI
[2024-01-24 14:20:42,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b7e8c8-f057-4836-b156-7ff07905d9ef/GCF_002091535.1_ASM209153v1_genomic.fna.gz --refList GCF_002091535.1_ASM209153v1_genomic.fna/target_genomes.txt --output GCF_002091535.1_ASM209153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:59,108] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:59,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:59,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:59,123] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:20:59,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:59,123] [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 chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	99.9994	2238	2241	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_003945765.1	333	587753	type	True	99.9992	2240	2241	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis		GCA_900625015.1	333	587753	type	True	99.9981	2238	2241	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	99.9972	2238	2241	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=ATCC 9446	GCA_002095925.1	333	587753	type	True	99.9918	2234	2241	95	conclusive
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	84.1338	1365	2241	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.8006	1138	2241	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.7303	1092	2241	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	82.1132	983	2241	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	81.575	991	2241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:59,125] [INFO] DFAST Taxonomy check result was written to GCF_002091535.1_ASM209153v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:59,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:59,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:59,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/checkm_data
[2024-01-24 14:20:59,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:59,193] [INFO] Task started: CheckM
[2024-01-24 14:20:59,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091535.1_ASM209153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091535.1_ASM209153v1_genomic.fna/checkm_input GCF_002091535.1_ASM209153v1_genomic.fna/checkm_result
[2024-01-24 14:22:02,048] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:02,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:02,071] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:02,071] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:02,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091535.1_ASM209153v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:02,072] [INFO] Task started: Blastn
[2024-01-24 14:22:02,072] [INFO] Running command: blastn -query GCF_002091535.1_ASM209153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9e1c7a9-9eac-4cee-bf0c-8900724920e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091535.1_ASM209153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:04,126] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:04,137] [INFO] Selected 7 target genomes.
[2024-01-24 14:22:04,138] [INFO] Target genome list was writen to GCF_002091535.1_ASM209153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:04,144] [INFO] Task started: fastANI
[2024-01-24 14:22:04,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b7e8c8-f057-4836-b156-7ff07905d9ef/GCF_002091535.1_ASM209153v1_genomic.fna.gz --refList GCF_002091535.1_ASM209153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091535.1_ASM209153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:17,610] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:17,620] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:22:17,620] [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_003945765.1	s__Pseudomonas_E chlororaphis	99.9992	2240	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	95.71	0.92	0.83	34	inconclusive
GCF_003850345.1	s__Pseudomonas_E chlororaphis_F	95.0218	1998	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.16	95.02	0.90	0.86	82	inconclusive
GCF_900107395.1	s__Pseudomonas_E sp900107395	93.5135	1905	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921865.1	s__Pseudomonas_E chlororaphis_D	91.3759	1813	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931465.1	s__Pseudomonas_E sp000931465	91.1486	1855	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
GCF_000397205.1	s__Pseudomonas_E protegens	86.6459	1631	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_003363755.1	s__Pseudomonas_E protegens_A	86.2151	1603	2241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.07	97.56	0.94	0.93	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:17,622] [INFO] GTDB search result was written to GCF_002091535.1_ASM209153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:17,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:17,625] [INFO] DFAST_QC result json was written to GCF_002091535.1_ASM209153v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:17,626] [INFO] DFAST_QC completed!
[2024-01-24 14:22:17,626] [INFO] Total running time: 0h2m1s