[2024-01-24 15:10:19,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference
[2024-01-24 15:10:22,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,727] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgb45c9a3e-78ac-4edf-9f96-6a39220d5597/GCF_025994255.1_ASM2599425v1_genomic.fna.gz | prodigal -d GCF_025994255.1_ASM2599425v1_genomic.fna/cds.fna -a GCF_025994255.1_ASM2599425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:29,935] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:29,935] [INFO] Task started: HMMsearch
[2024-01-24 15:10:29,935] [INFO] Running command: hmmsearch --tblout GCF_025994255.1_ASM2599425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/reference_markers.hmm GCF_025994255.1_ASM2599425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:30,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:30,175] [INFO] Found 6/6 markers.
[2024-01-24 15:10:30,201] [INFO] Query marker FASTA was written to GCF_025994255.1_ASM2599425v1_genomic.fna/markers.fasta
[2024-01-24 15:10:30,202] [INFO] Task started: Blastn
[2024-01-24 15:10:30,202] [INFO] Running command: blastn -query GCF_025994255.1_ASM2599425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/reference_markers.fasta -out GCF_025994255.1_ASM2599425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:30,905] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:30,909] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:30,909] [INFO] Target genome list was writen to GCF_025994255.1_ASM2599425v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:30,993] [INFO] Task started: fastANI
[2024-01-24 15:10:30,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45c9a3e-78ac-4edf-9f96-6a39220d5597/GCF_025994255.1_ASM2599425v1_genomic.fna.gz --refList GCF_025994255.1_ASM2599425v1_genomic.fna/target_genomes.txt --output GCF_025994255.1_ASM2599425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:39,011] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:39,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:39,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:39,024] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:39,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:39,025] [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
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	99.9708	773	790	95	conclusive
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	91.712	654	790	95	below_threshold
Neokomagataea tanensis	strain=AH13 = NBRC 106556	GCA_006542335.1	661191	661191	type	True	80.3141	366	790	95	below_threshold
Gluconobacter frateurii	strain=NBRC 3264	GCA_002723955.1	38308	38308	suspected-type	True	77.8919	126	790	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	77.6742	130	790	95	below_threshold
Gluconobacter thailandicus	strain=F149-1	GCA_000964465.1	257438	257438	type	True	77.6227	119	790	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	77.5097	125	790	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	77.3512	115	790	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	76.4341	61	790	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	76.403	62	790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:39,026] [INFO] DFAST Taxonomy check result was written to GCF_025994255.1_ASM2599425v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:39,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:39,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:39,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/checkm_data
[2024-01-24 15:10:39,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:39,055] [INFO] Task started: CheckM
[2024-01-24 15:10:39,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994255.1_ASM2599425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994255.1_ASM2599425v1_genomic.fna/checkm_input GCF_025994255.1_ASM2599425v1_genomic.fna/checkm_result
[2024-01-24 15:11:06,966] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:06,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,986] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:06,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:06,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994255.1_ASM2599425v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:06,987] [INFO] Task started: Blastn
[2024-01-24 15:11:06,987] [INFO] Running command: blastn -query GCF_025994255.1_ASM2599425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4668489a-7c2b-47b1-98f9-f0cee875ef37/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994255.1_ASM2599425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:08,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:08,158] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:08,158] [INFO] Target genome list was writen to GCF_025994255.1_ASM2599425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:08,180] [INFO] Task started: fastANI
[2024-01-24 15:11:08,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45c9a3e-78ac-4edf-9f96-6a39220d5597/GCF_025994255.1_ASM2599425v1_genomic.fna.gz --refList GCF_025994255.1_ASM2599425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994255.1_ASM2599425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:15,280] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:15,290] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:15,290] [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_001598495.1	s__Neokomagataea thailandica	99.9708	773	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018122595.1	s__Neokomagataea sp018122595	91.7651	652	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542335.1	s__Neokomagataea tanensis	80.3141	366	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014132155.1	s__Gluconobacter_A sp014132155	77.8922	132	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.46	96.68	0.90	0.89	4	-
GCF_002723955.1	s__Gluconobacter_A frateurii	77.8919	126	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	97.06	97.06	0.93	0.93	2	-
GCF_002723975.1	s__Gluconobacter_A japonicus	77.6991	129	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	96.84	95.27	0.89	0.85	9	-
GCF_000964465.1	s__Gluconobacter_A thailandicus	77.6497	118	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_A	95.0	98.77	97.43	0.93	0.88	11	-
GCF_002723995.1	s__Gluconobacter kondonii	77.5202	124	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	-
GCF_002723915.1	s__Gluconobacter albidus	77.3373	114	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_001581005.1	s__Acetobacter orleanensis	76.3906	61	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:15,292] [INFO] GTDB search result was written to GCF_025994255.1_ASM2599425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:15,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:15,295] [INFO] DFAST_QC result json was written to GCF_025994255.1_ASM2599425v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:15,296] [INFO] DFAST_QC completed!
[2024-01-24 15:11:15,296] [INFO] Total running time: 0h0m55s