[2024-01-24 10:47:06,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference
[2024-01-24 10:47:12,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77ea5b3-fe55-4854-9bb6-9b3f99d2cfe7/GCF_015244705.1_ASM1524470v1_genomic.fna.gz | prodigal -d GCF_015244705.1_ASM1524470v1_genomic.fna/cds.fna -a GCF_015244705.1_ASM1524470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,940] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,940] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,940] [INFO] Running command: hmmsearch --tblout GCF_015244705.1_ASM1524470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/reference_markers.hmm GCF_015244705.1_ASM1524470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,177] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,179] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,209] [INFO] Query marker FASTA was written to GCF_015244705.1_ASM1524470v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,209] [INFO] Task started: Blastn
[2024-01-24 10:47:22,209] [INFO] Running command: blastn -query GCF_015244705.1_ASM1524470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/reference_markers.fasta -out GCF_015244705.1_ASM1524470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,923] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,926] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:22,926] [INFO] Target genome list was writen to GCF_015244705.1_ASM1524470v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,954] [INFO] Task started: fastANI
[2024-01-24 10:47:22,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77ea5b3-fe55-4854-9bb6-9b3f99d2cfe7/GCF_015244705.1_ASM1524470v1_genomic.fna.gz --refList GCF_015244705.1_ASM1524470v1_genomic.fna/target_genomes.txt --output GCF_015244705.1_ASM1524470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:30,358] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:30,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:30,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:30,369] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:30,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:30,369] [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 potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	100.0	1107	1109	95	conclusive
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	96.8657	921	1109	95	conclusive
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	94.5789	768	1109	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	94.4497	798	1109	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	94.448	797	1109	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	91.8871	777	1109	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	89.8596	797	1109	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.845	191	1109	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.7994	187	1109	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0509	81	1109	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:30,371] [INFO] DFAST Taxonomy check result was written to GCF_015244705.1_ASM1524470v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:30,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:30,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:30,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/checkm_data
[2024-01-24 10:47:30,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:30,412] [INFO] Task started: CheckM
[2024-01-24 10:47:30,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015244705.1_ASM1524470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015244705.1_ASM1524470v1_genomic.fna/checkm_input GCF_015244705.1_ASM1524470v1_genomic.fna/checkm_result
[2024-01-24 10:48:02,734] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:02,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,753] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:02,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:02,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015244705.1_ASM1524470v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:02,754] [INFO] Task started: Blastn
[2024-01-24 10:48:02,754] [INFO] Running command: blastn -query GCF_015244705.1_ASM1524470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65620bee-12f5-4bf4-b9f6-83b9ced843b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_015244705.1_ASM1524470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:03,974] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:03,978] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:03,978] [INFO] Target genome list was writen to GCF_015244705.1_ASM1524470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:03,983] [INFO] Task started: fastANI
[2024-01-24 10:48:03,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77ea5b3-fe55-4854-9bb6-9b3f99d2cfe7/GCF_015244705.1_ASM1524470v1_genomic.fna.gz --refList GCF_015244705.1_ASM1524470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015244705.1_ASM1524470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:09,193] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,200] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:09,200] [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_001580675.1	s__Gluconobacter potus	96.8657	921	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	conclusive
GCF_006539685.1	s__Gluconobacter oxydans	94.5789	768	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_018811945.1	s__Gluconobacter sp018811945	92.7304	888	1109	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	91.8871	777	1109	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	90.1116	782	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
GCF_015244565.1	s__Gluconobacter vitians	89.8762	796	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	89.8512	766	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,202] [INFO] GTDB search result was written to GCF_015244705.1_ASM1524470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:09,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:09,205] [INFO] DFAST_QC result json was written to GCF_015244705.1_ASM1524470v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:09,206] [INFO] DFAST_QC completed!
[2024-01-24 10:48:09,206] [INFO] Total running time: 0h1m3s