[2024-01-24 14:12:04,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:04,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:04,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference
[2024-01-24 14:12:05,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,767] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,767] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd69a18a-b1bb-410a-8aa4-71615563eb73/GCF_001267175.1_ASM126717v1_genomic.fna.gz | prodigal -d GCF_001267175.1_ASM126717v1_genomic.fna/cds.fna -a GCF_001267175.1_ASM126717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:11,521] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:11,521] [INFO] Task started: HMMsearch
[2024-01-24 14:12:11,521] [INFO] Running command: hmmsearch --tblout GCF_001267175.1_ASM126717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/reference_markers.hmm GCF_001267175.1_ASM126717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:11,794] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:11,797] [INFO] Found 6/6 markers.
[2024-01-24 14:12:11,830] [INFO] Query marker FASTA was written to GCF_001267175.1_ASM126717v1_genomic.fna/markers.fasta
[2024-01-24 14:12:11,831] [INFO] Task started: Blastn
[2024-01-24 14:12:11,831] [INFO] Running command: blastn -query GCF_001267175.1_ASM126717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/reference_markers.fasta -out GCF_001267175.1_ASM126717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:12,551] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:12,554] [INFO] Selected 31 target genomes.
[2024-01-24 14:12:12,555] [INFO] Target genome list was writen to GCF_001267175.1_ASM126717v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:12,582] [INFO] Task started: fastANI
[2024-01-24 14:12:12,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd69a18a-b1bb-410a-8aa4-71615563eb73/GCF_001267175.1_ASM126717v1_genomic.fna.gz --refList GCF_001267175.1_ASM126717v1_genomic.fna/target_genomes.txt --output GCF_001267175.1_ASM126717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:32,521] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:32,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:32,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:32,527] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:32,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:32,527] [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
Thiopseudomonas alkaliphila	strain=B4199	GCA_001267175.1	1697053	1697053	type	True	100.0	829	831	95	conclusive
Denitrificimonas caeni	strain=DSM 24390	GCA_000421765.1	521720	521720	type	True	78.3072	141	831	95	below_threshold
Pseudomonas endophytica	strain=BSTT44	GCA_001411475.1	1563157	1563157	type	True	76.7439	58	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:32,529] [INFO] DFAST Taxonomy check result was written to GCF_001267175.1_ASM126717v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:32,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:32,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:32,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/checkm_data
[2024-01-24 14:12:32,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:32,559] [INFO] Task started: CheckM
[2024-01-24 14:12:32,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001267175.1_ASM126717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001267175.1_ASM126717v1_genomic.fna/checkm_input GCF_001267175.1_ASM126717v1_genomic.fna/checkm_result
[2024-01-24 14:12:56,147] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:56,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:56,171] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:56,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:56,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001267175.1_ASM126717v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:56,172] [INFO] Task started: Blastn
[2024-01-24 14:12:56,172] [INFO] Running command: blastn -query GCF_001267175.1_ASM126717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg684d46d7-cfcd-4f37-9796-39b175bf6f35/dqc_reference/reference_markers_gtdb.fasta -out GCF_001267175.1_ASM126717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:57,105] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:57,108] [INFO] Selected 20 target genomes.
[2024-01-24 14:12:57,109] [INFO] Target genome list was writen to GCF_001267175.1_ASM126717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:57,139] [INFO] Task started: fastANI
[2024-01-24 14:12:57,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd69a18a-b1bb-410a-8aa4-71615563eb73/GCF_001267175.1_ASM126717v1_genomic.fna.gz --refList GCF_001267175.1_ASM126717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001267175.1_ASM126717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:08,817] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:08,831] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:08,832] [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_001267175.1	s__Oblitimonas alkaliphila	100.0	829	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Oblitimonas	95.0	98.77	98.36	0.92	0.89	8	conclusive
GCF_008807395.1	s__Pseudomonas_C sp002342705	78.9836	164	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.04	98.98	0.93	0.92	7	-
GCF_000421765.1	s__Pseudomonas_C caeni	78.3216	140	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	96.77	96.34	0.93	0.85	7	-
GCF_905120345.1	s__Pseudomonas_C caeni_A	78.0288	150	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719655.1	s__Pseudomonas_C sp012719655	77.7531	120	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728315.1	s__Pseudomonas_C sp012728315	77.7184	140	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513025.1	s__Pseudomonas_C sp001513025	77.4114	144	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.84	99.84	0.94	0.94	2	-
GCA_012728415.1	s__Thiopseudomonas sp012728415	77.1344	58	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513235.1	s__Pseudomonas_C sp012513235	76.9014	93	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001411475.1	s__Pseudomonas_E endophytica	76.7439	58	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518175.1	s__Pseudomonas_C sp012518175	76.7364	107	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:08,833] [INFO] GTDB search result was written to GCF_001267175.1_ASM126717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:08,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:08,838] [INFO] DFAST_QC result json was written to GCF_001267175.1_ASM126717v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:08,838] [INFO] DFAST_QC completed!
[2024-01-24 14:13:08,838] [INFO] Total running time: 0h1m4s