[2024-01-25 18:04:20,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:20,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:20,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference
[2024-01-25 18:04:21,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:21,649] [INFO] Task started: Prodigal
[2024-01-25 18:04:21,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg57b3e26f-ed34-4d37-abeb-c48dedf66a7b/GCF_015244675.1_ASM1524467v1_genomic.fna.gz | prodigal -d GCF_015244675.1_ASM1524467v1_genomic.fna/cds.fna -a GCF_015244675.1_ASM1524467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:29,231] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:29,231] [INFO] Task started: HMMsearch
[2024-01-25 18:04:29,231] [INFO] Running command: hmmsearch --tblout GCF_015244675.1_ASM1524467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/reference_markers.hmm GCF_015244675.1_ASM1524467v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:29,431] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:29,432] [INFO] Found 6/6 markers.
[2024-01-25 18:04:29,457] [INFO] Query marker FASTA was written to GCF_015244675.1_ASM1524467v1_genomic.fna/markers.fasta
[2024-01-25 18:04:29,457] [INFO] Task started: Blastn
[2024-01-25 18:04:29,457] [INFO] Running command: blastn -query GCF_015244675.1_ASM1524467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/reference_markers.fasta -out GCF_015244675.1_ASM1524467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:30,161] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:30,164] [INFO] Selected 10 target genomes.
[2024-01-25 18:04:30,165] [INFO] Target genome list was writen to GCF_015244675.1_ASM1524467v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:30,175] [INFO] Task started: fastANI
[2024-01-25 18:04:30,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b3e26f-ed34-4d37-abeb-c48dedf66a7b/GCF_015244675.1_ASM1524467v1_genomic.fna.gz --refList GCF_015244675.1_ASM1524467v1_genomic.fna/target_genomes.txt --output GCF_015244675.1_ASM1524467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:37,601] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:37,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:37,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:37,608] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:04:37,608] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:37,608] [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
Gluconobacter cerevisiae	strain=LMG 27748	GCA_015244675.1	1379734	1379734	type	True	100.0	981	982	95	conclusive
Gluconobacter cerevisiae	strain=DSM 27644	GCA_018811965.1	1379734	1379734	type	True	99.9893	977	982	95	conclusive
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	91.3611	819	982	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	90.7251	824	982	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	89.5974	795	982	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	86.0552	712	982	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	85.6315	724	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:37,609] [INFO] DFAST Taxonomy check result was written to GCF_015244675.1_ASM1524467v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:37,610] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:37,610] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:37,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/checkm_data
[2024-01-25 18:04:37,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:37,645] [INFO] Task started: CheckM
[2024-01-25 18:04:37,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015244675.1_ASM1524467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015244675.1_ASM1524467v1_genomic.fna/checkm_input GCF_015244675.1_ASM1524467v1_genomic.fna/checkm_result
[2024-01-25 18:05:03,881] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:03,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:03,896] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:03,896] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:03,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015244675.1_ASM1524467v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:03,897] [INFO] Task started: Blastn
[2024-01-25 18:05:03,897] [INFO] Running command: blastn -query GCF_015244675.1_ASM1524467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c193df5-9867-4c04-ab0c-1ef6a04eea2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015244675.1_ASM1524467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:05,144] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:05,149] [INFO] Selected 8 target genomes.
[2024-01-25 18:05:05,149] [INFO] Target genome list was writen to GCF_015244675.1_ASM1524467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:05,156] [INFO] Task started: fastANI
[2024-01-25 18:05:05,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b3e26f-ed34-4d37-abeb-c48dedf66a7b/GCF_015244675.1_ASM1524467v1_genomic.fna.gz --refList GCF_015244675.1_ASM1524467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015244675.1_ASM1524467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:11,103] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:11,109] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:11,109] [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_015244675.1	s__Gluconobacter cerevisiae	100.0	981	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_002723995.1	s__Gluconobacter kondonii	91.3786	818	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	-
GCF_015244745.1	s__Gluconobacter cadivus	90.7085	825	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
GCF_002723915.1	s__Gluconobacter albidus	89.5974	795	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_018256155.1	s__Gluconobacter sp018256155	86.1742	721	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009547075.1	s__Gluconobacter sp009547075	86.0552	712	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244565.1	s__Gluconobacter vitians	85.7196	720	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539125.1	s__Gluconobacter sphaericus	85.2502	668	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:11,112] [INFO] GTDB search result was written to GCF_015244675.1_ASM1524467v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:11,113] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:11,118] [INFO] DFAST_QC result json was written to GCF_015244675.1_ASM1524467v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:11,119] [INFO] DFAST_QC completed!
[2024-01-25 18:05:11,119] [INFO] Total running time: 0h0m51s