[2024-01-25 18:10:20,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:20,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:20,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference
[2024-01-25 18:10:21,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:21,632] [INFO] Task started: Prodigal
[2024-01-25 18:10:21,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg856668c1-1b1d-4801-97e8-f40771c0a006/GCF_025994295.1_ASM2599429v1_genomic.fna.gz | prodigal -d GCF_025994295.1_ASM2599429v1_genomic.fna/cds.fna -a GCF_025994295.1_ASM2599429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:27,408] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:27,408] [INFO] Task started: HMMsearch
[2024-01-25 18:10:27,408] [INFO] Running command: hmmsearch --tblout GCF_025994295.1_ASM2599429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/reference_markers.hmm GCF_025994295.1_ASM2599429v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:27,590] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:27,591] [INFO] Found 6/6 markers.
[2024-01-25 18:10:27,613] [INFO] Query marker FASTA was written to GCF_025994295.1_ASM2599429v1_genomic.fna/markers.fasta
[2024-01-25 18:10:27,613] [INFO] Task started: Blastn
[2024-01-25 18:10:27,613] [INFO] Running command: blastn -query GCF_025994295.1_ASM2599429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/reference_markers.fasta -out GCF_025994295.1_ASM2599429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:28,245] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:28,248] [INFO] Selected 18 target genomes.
[2024-01-25 18:10:28,248] [INFO] Target genome list was writen to GCF_025994295.1_ASM2599429v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:28,269] [INFO] Task started: fastANI
[2024-01-25 18:10:28,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg856668c1-1b1d-4801-97e8-f40771c0a006/GCF_025994295.1_ASM2599429v1_genomic.fna.gz --refList GCF_025994295.1_ASM2599429v1_genomic.fna/target_genomes.txt --output GCF_025994295.1_ASM2599429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:34,835] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:34,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:34,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:34,842] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:34,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:34,842] [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
Saccharibacter floricola	strain=DSM 15669	GCA_000378165.1	231053	231053	type	True	99.9914	750	754	95	conclusive
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	77.5679	96	754	95	below_threshold
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	77.5587	83	754	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	77.5582	94	754	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	77.5399	84	754	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	76.7879	63	754	95	below_threshold
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	76.6575	65	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:34,844] [INFO] DFAST Taxonomy check result was written to GCF_025994295.1_ASM2599429v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:34,844] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:34,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:34,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/checkm_data
[2024-01-25 18:10:34,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:34,871] [INFO] Task started: CheckM
[2024-01-25 18:10:34,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994295.1_ASM2599429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994295.1_ASM2599429v1_genomic.fna/checkm_input GCF_025994295.1_ASM2599429v1_genomic.fna/checkm_result
[2024-01-25 18:10:56,797] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:56,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:56,813] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:56,814] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:56,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994295.1_ASM2599429v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:56,814] [INFO] Task started: Blastn
[2024-01-25 18:10:56,814] [INFO] Running command: blastn -query GCF_025994295.1_ASM2599429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766e90cb-5573-45bc-aab5-1ff8a31c2f6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994295.1_ASM2599429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:57,859] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:57,863] [INFO] Selected 15 target genomes.
[2024-01-25 18:10:57,863] [INFO] Target genome list was writen to GCF_025994295.1_ASM2599429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:57,910] [INFO] Task started: fastANI
[2024-01-25 18:10:57,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg856668c1-1b1d-4801-97e8-f40771c0a006/GCF_025994295.1_ASM2599429v1_genomic.fna.gz --refList GCF_025994295.1_ASM2599429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994295.1_ASM2599429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:04,164] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:04,171] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:04,172] [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_000378165.1	s__Saccharibacter floricola	99.9914	750	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009834765.1	s__Saccharibacter sp009834765	92.9883	681	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	99.99	99.98	0.99	0.99	3	-
GCF_009834805.1	s__Saccharibacter sp009834805	77.8402	147	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221685.1	s__Bombella apis	77.5721	83	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_002003665.1	s__Bombella intestini	77.5582	94	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014048475.1	s__Bombella favorum	77.5401	97	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725755.1	s__Bombella sp009725755	77.3845	119	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_014048465.1	s__Bombella mellum	77.2087	84	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592045.1	s__Bombella apium_A	77.188	110	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122595.1	s__Neokomagataea sp018122595	76.7535	63	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598495.1	s__Neokomagataea thailandica	76.5988	67	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:04,173] [INFO] GTDB search result was written to GCF_025994295.1_ASM2599429v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:04,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:04,178] [INFO] DFAST_QC result json was written to GCF_025994295.1_ASM2599429v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:04,178] [INFO] DFAST_QC completed!
[2024-01-25 18:11:04,178] [INFO] Total running time: 0h0m44s