[2024-01-24 13:57:44,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference
[2024-01-24 13:57:46,127] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,128] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg31a7eee7-6c70-494a-bc6b-10c9074b0a90/GCF_003699065.1_ASM369906v1_genomic.fna.gz | prodigal -d GCF_003699065.1_ASM369906v1_genomic.fna/cds.fna -a GCF_003699065.1_ASM369906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:06,792] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:06,792] [INFO] Task started: HMMsearch
[2024-01-24 13:58:06,792] [INFO] Running command: hmmsearch --tblout GCF_003699065.1_ASM369906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/reference_markers.hmm GCF_003699065.1_ASM369906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:07,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:07,112] [INFO] Found 6/6 markers.
[2024-01-24 13:58:07,163] [INFO] Query marker FASTA was written to GCF_003699065.1_ASM369906v1_genomic.fna/markers.fasta
[2024-01-24 13:58:07,164] [INFO] Task started: Blastn
[2024-01-24 13:58:07,164] [INFO] Running command: blastn -query GCF_003699065.1_ASM369906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/reference_markers.fasta -out GCF_003699065.1_ASM369906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:08,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:08,233] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:08,234] [INFO] Target genome list was writen to GCF_003699065.1_ASM369906v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:08,245] [INFO] Task started: fastANI
[2024-01-24 13:58:08,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a7eee7-6c70-494a-bc6b-10c9074b0a90/GCF_003699065.1_ASM369906v1_genomic.fna.gz --refList GCF_003699065.1_ASM369906v1_genomic.fna/target_genomes.txt --output GCF_003699065.1_ASM369906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:24,419] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:24,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:24,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:24,429] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:24,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:24,430] [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 corrugata	strain=NCPPB2445	GCA_003699065.1	47879	47879	type	True	100.0	1949	1955	95	conclusive
Pseudomonas corrugata	strain=DSM 7228	GCA_001269905.1	47879	47879	type	True	99.9925	1953	1955	95	conclusive
Pseudomonas corrugata	strain=NCPPB2445	GCA_001411965.1	47879	47879	type	True	99.9912	1952	1955	95	conclusive
Pseudomonas mediterranea	strain=CFBP 5447	GCA_000774145.1	183795	183795	type	True	92.8438	1724	1955	95	below_threshold
Pseudomonas mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	92.8319	1750	1955	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	86.8486	1494	1955	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	83.8631	1208	1955	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	83.8107	1204	1955	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	82.9601	1195	1955	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.6033	800	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:24,431] [INFO] DFAST Taxonomy check result was written to GCF_003699065.1_ASM369906v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:24,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:24,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:24,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/checkm_data
[2024-01-24 13:58:24,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:24,492] [INFO] Task started: CheckM
[2024-01-24 13:58:24,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003699065.1_ASM369906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003699065.1_ASM369906v1_genomic.fna/checkm_input GCF_003699065.1_ASM369906v1_genomic.fna/checkm_result
[2024-01-24 13:59:22,084] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:22,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,107] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:22,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:22,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003699065.1_ASM369906v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:22,108] [INFO] Task started: Blastn
[2024-01-24 13:59:22,108] [INFO] Running command: blastn -query GCF_003699065.1_ASM369906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7420d7a1-e966-4fba-b14d-88be179cbbce/dqc_reference/reference_markers_gtdb.fasta -out GCF_003699065.1_ASM369906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:23,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:23,927] [INFO] Selected 5 target genomes.
[2024-01-24 13:59:23,927] [INFO] Target genome list was writen to GCF_003699065.1_ASM369906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:23,933] [INFO] Task started: fastANI
[2024-01-24 13:59:23,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a7eee7-6c70-494a-bc6b-10c9074b0a90/GCF_003699065.1_ASM369906v1_genomic.fna.gz --refList GCF_003699065.1_ASM369906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003699065.1_ASM369906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:34,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:34,616] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:34,616] [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_001269905.1	s__Pseudomonas_E corrugata	99.9925	1953	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.47	0.98	0.95	7	conclusive
GCF_006227205.1	s__Pseudomonas_E sp006227205	94.1593	1788	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.77	0.93	0.93	3	-
GCF_014596565.1	s__Pseudomonas_E sp000801235	93.2564	1728	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000774145.1	s__Pseudomonas_E mediterranea	92.8438	1724	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.46	99.30	0.95	0.94	8	-
GCF_007828215.1	s__Pseudomonas_E sp007828215	92.2315	1665	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	99.65	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:34,618] [INFO] GTDB search result was written to GCF_003699065.1_ASM369906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:34,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:34,624] [INFO] DFAST_QC result json was written to GCF_003699065.1_ASM369906v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:34,624] [INFO] DFAST_QC completed!
[2024-01-24 13:59:34,625] [INFO] Total running time: 0h1m50s