[2024-01-24 10:57:21,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:21,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:21,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference
[2024-01-24 10:57:23,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:23,099] [INFO] Task started: Prodigal
[2024-01-24 10:57:23,100] [INFO] Running command: gunzip -c /var/lib/cwl/stgb67610a5-d52e-42bf-aab4-eff4bd588ae9/GCF_026385485.1_ASM2638548v1_genomic.fna.gz | prodigal -d GCF_026385485.1_ASM2638548v1_genomic.fna/cds.fna -a GCF_026385485.1_ASM2638548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:28,306] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:28,306] [INFO] Task started: HMMsearch
[2024-01-24 10:57:28,306] [INFO] Running command: hmmsearch --tblout GCF_026385485.1_ASM2638548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/reference_markers.hmm GCF_026385485.1_ASM2638548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:28,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:28,608] [INFO] Found 6/6 markers.
[2024-01-24 10:57:28,640] [INFO] Query marker FASTA was written to GCF_026385485.1_ASM2638548v1_genomic.fna/markers.fasta
[2024-01-24 10:57:28,642] [INFO] Task started: Blastn
[2024-01-24 10:57:28,642] [INFO] Running command: blastn -query GCF_026385485.1_ASM2638548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/reference_markers.fasta -out GCF_026385485.1_ASM2638548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:29,434] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:29,438] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:29,438] [INFO] Target genome list was writen to GCF_026385485.1_ASM2638548v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:29,552] [INFO] Task started: fastANI
[2024-01-24 10:57:29,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67610a5-d52e-42bf-aab4-eff4bd588ae9/GCF_026385485.1_ASM2638548v1_genomic.fna.gz --refList GCF_026385485.1_ASM2638548v1_genomic.fna/target_genomes.txt --output GCF_026385485.1_ASM2638548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:37,074] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:37,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:37,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:37,123] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:37,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:37,124] [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
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	78.4874	225	619	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	78.4469	251	619	95	below_threshold
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	78.4285	268	619	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	78.391	226	619	95	below_threshold
Saccharibacter floricola	strain=DSM 15669	GCA_000378165.1	231053	231053	type	True	77.4628	114	619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:37,129] [INFO] DFAST Taxonomy check result was written to GCF_026385485.1_ASM2638548v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:37,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:37,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:37,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/checkm_data
[2024-01-24 10:57:37,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:37,189] [INFO] Task started: CheckM
[2024-01-24 10:57:37,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026385485.1_ASM2638548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026385485.1_ASM2638548v1_genomic.fna/checkm_input GCF_026385485.1_ASM2638548v1_genomic.fna/checkm_result
[2024-01-24 10:57:59,712] [INFO] Task succeeded: CheckM
[2024-01-24 10:57:59,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:57:59,731] [INFO] ===== Completeness check finished =====
[2024-01-24 10:57:59,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:57:59,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026385485.1_ASM2638548v1_genomic.fna/markers.fasta)
[2024-01-24 10:57:59,732] [INFO] Task started: Blastn
[2024-01-24 10:57:59,732] [INFO] Running command: blastn -query GCF_026385485.1_ASM2638548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07b23a81-2cff-4f24-bf5f-e8d389c0fedd/dqc_reference/reference_markers_gtdb.fasta -out GCF_026385485.1_ASM2638548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:00,950] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:00,954] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:00,954] [INFO] Target genome list was writen to GCF_026385485.1_ASM2638548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:00,963] [INFO] Task started: fastANI
[2024-01-24 10:58:00,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67610a5-d52e-42bf-aab4-eff4bd588ae9/GCF_026385485.1_ASM2638548v1_genomic.fna.gz --refList GCF_026385485.1_ASM2638548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026385485.1_ASM2638548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:05,561] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:05,580] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:05,581] [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_009725755.1	s__Bombella sp009725755	99.3221	604	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	conclusive
GCF_002592045.1	s__Bombella apium_A	94.9248	566	619	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	78.4331	267	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002003665.1	s__Bombella intestini	78.4306	252	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221685.1	s__Bombella apis	78.391	226	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048465.1	s__Bombella mellum	78.3287	225	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834765.1	s__Saccharibacter sp009834765	77.4389	117	619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	99.99	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:05,583] [INFO] GTDB search result was written to GCF_026385485.1_ASM2638548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:05,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:05,587] [INFO] DFAST_QC result json was written to GCF_026385485.1_ASM2638548v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:05,587] [INFO] DFAST_QC completed!
[2024-01-24 10:58:05,587] [INFO] Total running time: 0h0m44s