[2024-01-24 11:20:19,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference
[2024-01-24 11:20:20,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,886] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,886] [INFO] Running command: gunzip -c /var/lib/cwl/stge66fce00-45c3-43fc-ad7e-b6e3378955c1/GCF_025996295.1_ASM2599629v1_genomic.fna.gz | prodigal -d GCF_025996295.1_ASM2599629v1_genomic.fna/cds.fna -a GCF_025996295.1_ASM2599629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:29,120] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:29,121] [INFO] Task started: HMMsearch
[2024-01-24 11:20:29,121] [INFO] Running command: hmmsearch --tblout GCF_025996295.1_ASM2599629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/reference_markers.hmm GCF_025996295.1_ASM2599629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:29,393] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:29,394] [INFO] Found 6/6 markers.
[2024-01-24 11:20:29,427] [INFO] Query marker FASTA was written to GCF_025996295.1_ASM2599629v1_genomic.fna/markers.fasta
[2024-01-24 11:20:29,427] [INFO] Task started: Blastn
[2024-01-24 11:20:29,427] [INFO] Running command: blastn -query GCF_025996295.1_ASM2599629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/reference_markers.fasta -out GCF_025996295.1_ASM2599629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:30,186] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:30,190] [INFO] Selected 16 target genomes.
[2024-01-24 11:20:30,190] [INFO] Target genome list was writen to GCF_025996295.1_ASM2599629v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:30,198] [INFO] Task started: fastANI
[2024-01-24 11:20:30,198] [INFO] Running command: fastANI --query /var/lib/cwl/stge66fce00-45c3-43fc-ad7e-b6e3378955c1/GCF_025996295.1_ASM2599629v1_genomic.fna.gz --refList GCF_025996295.1_ASM2599629v1_genomic.fna/target_genomes.txt --output GCF_025996295.1_ASM2599629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:40,076] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:40,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:40,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:40,096] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:40,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:40,097] [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 kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	99.9806	940	956	95	conclusive
Gluconobacter sphaericus	strain=LMG1414	GCA_015244605.1	574987	574987	type	True	86.3261	664	956	95	below_threshold
Gluconobacter sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	86.251	660	956	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	85.6922	654	956	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	85.6254	672	956	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	85.3731	652	956	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	85.0794	633	956	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	85.0571	641	956	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	84.9839	656	956	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	84.9041	639	956	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	84.866	663	956	95	below_threshold
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	84.7214	641	956	95	below_threshold
Gluconobacter morbifer	strain=G707	GCA_000234355.2	479935	479935	type	True	79.4346	392	956	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.675	152	956	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.2752	63	956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:40,098] [INFO] DFAST Taxonomy check result was written to GCF_025996295.1_ASM2599629v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:40,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:40,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:40,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/checkm_data
[2024-01-24 11:20:40,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:40,128] [INFO] Task started: CheckM
[2024-01-24 11:20:40,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025996295.1_ASM2599629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025996295.1_ASM2599629v1_genomic.fna/checkm_input GCF_025996295.1_ASM2599629v1_genomic.fna/checkm_result
[2024-01-24 11:21:09,816] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:09,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:09,838] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:09,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:09,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025996295.1_ASM2599629v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:09,839] [INFO] Task started: Blastn
[2024-01-24 11:21:09,839] [INFO] Running command: blastn -query GCF_025996295.1_ASM2599629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9016b7ca-c01c-42a9-8df2-abe993e65ce9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025996295.1_ASM2599629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:11,048] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:11,051] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:11,051] [INFO] Target genome list was writen to GCF_025996295.1_ASM2599629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:11,060] [INFO] Task started: fastANI
[2024-01-24 11:21:11,060] [INFO] Running command: fastANI --query /var/lib/cwl/stge66fce00-45c3-43fc-ad7e-b6e3378955c1/GCF_025996295.1_ASM2599629v1_genomic.fna.gz --refList GCF_025996295.1_ASM2599629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025996295.1_ASM2599629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:20,153] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:20,168] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:20,168] [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_007988905.1	s__Gluconobacter kanchanaburiensis	99.9806	940	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006539125.1	s__Gluconobacter sphaericus	86.251	660	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
GCF_002723915.1	s__Gluconobacter albidus	85.8321	668	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_009547075.1	s__Gluconobacter sp009547075	85.7092	653	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244745.1	s__Gluconobacter cadivus	85.6231	672	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
GCF_002723995.1	s__Gluconobacter kondonii	85.3731	652	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	-
GCF_015244675.1	s__Gluconobacter cerevisiae	85.107	632	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006539685.1	s__Gluconobacter oxydans	85.0794	633	956	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	85.0591	661	956	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	84.9775	657	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580675.1	s__Gluconobacter potus	84.9173	638	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_018256155.1	s__Gluconobacter sp018256155	84.8397	646	956	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	84.719	641	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000234355.1	s__Gluconobacter_C morbifer	79.4479	391	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,170] [INFO] GTDB search result was written to GCF_025996295.1_ASM2599629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:20,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:20,174] [INFO] DFAST_QC result json was written to GCF_025996295.1_ASM2599629v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:20,174] [INFO] DFAST_QC completed!
[2024-01-24 11:21:20,174] [INFO] Total running time: 0h1m1s