[2024-01-24 13:01:20,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:20,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:20,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference
[2024-01-24 13:01:21,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,803] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg23672ccd-b4cc-4a5c-87b6-6db03a2c1b30/GCF_006539125.1_ASM653912v1_genomic.fna.gz | prodigal -d GCF_006539125.1_ASM653912v1_genomic.fna/cds.fna -a GCF_006539125.1_ASM653912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:30,729] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:30,729] [INFO] Task started: HMMsearch
[2024-01-24 13:01:30,730] [INFO] Running command: hmmsearch --tblout GCF_006539125.1_ASM653912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/reference_markers.hmm GCF_006539125.1_ASM653912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:30,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:30,978] [INFO] Found 6/6 markers.
[2024-01-24 13:01:31,014] [INFO] Query marker FASTA was written to GCF_006539125.1_ASM653912v1_genomic.fna/markers.fasta
[2024-01-24 13:01:31,015] [INFO] Task started: Blastn
[2024-01-24 13:01:31,015] [INFO] Running command: blastn -query GCF_006539125.1_ASM653912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/reference_markers.fasta -out GCF_006539125.1_ASM653912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:31,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:31,827] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:31,828] [INFO] Target genome list was writen to GCF_006539125.1_ASM653912v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:31,837] [INFO] Task started: fastANI
[2024-01-24 13:01:31,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg23672ccd-b4cc-4a5c-87b6-6db03a2c1b30/GCF_006539125.1_ASM653912v1_genomic.fna.gz --refList GCF_006539125.1_ASM653912v1_genomic.fna/target_genomes.txt --output GCF_006539125.1_ASM653912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:41,872] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:41,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:41,892] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:41,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:41,893] [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 sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	100.0	968	972	95	conclusive
Gluconobacter sphaericus	strain=LMG1414	GCA_015244605.1	574987	574987	type	True	99.9995	967	972	95	conclusive
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	90.6291	731	972	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	90.5975	742	972	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	90.5946	747	972	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	90.1891	763	972	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	90.1307	771	972	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	89.4262	750	972	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	87.1288	700	972	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	86.5332	708	972	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	86.1704	693	972	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	86.072	713	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,896] [INFO] DFAST Taxonomy check result was written to GCF_006539125.1_ASM653912v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:41,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:41,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:41,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/checkm_data
[2024-01-24 13:01:41,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:41,935] [INFO] Task started: CheckM
[2024-01-24 13:01:41,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539125.1_ASM653912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539125.1_ASM653912v1_genomic.fna/checkm_input GCF_006539125.1_ASM653912v1_genomic.fna/checkm_result
[2024-01-24 13:02:11,908] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:11,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:11,931] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:11,931] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:11,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539125.1_ASM653912v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:11,932] [INFO] Task started: Blastn
[2024-01-24 13:02:11,932] [INFO] Running command: blastn -query GCF_006539125.1_ASM653912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044124b8-d464-4184-a92b-7794fb204540/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539125.1_ASM653912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:13,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:13,281] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:13,281] [INFO] Target genome list was writen to GCF_006539125.1_ASM653912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:13,306] [INFO] Task started: fastANI
[2024-01-24 13:02:13,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg23672ccd-b4cc-4a5c-87b6-6db03a2c1b30/GCF_006539125.1_ASM653912v1_genomic.fna.gz --refList GCF_006539125.1_ASM653912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539125.1_ASM653912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:20,838] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,848] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:20,848] [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_006539125.1	s__Gluconobacter sphaericus	100.0	968	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	conclusive
GCF_006539685.1	s__Gluconobacter oxydans	90.6291	731	972	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	90.2455	785	972	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	90.1684	764	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_009547075.1	s__Gluconobacter sp009547075	89.4209	750	972	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	87.127	700	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723915.1	s__Gluconobacter albidus	86.5194	709	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_007988905.1	s__Gluconobacter kanchanaburiensis	86.221	665	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002723995.1	s__Gluconobacter kondonii	86.1699	693	972	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	86.0523	714	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
GCF_015244675.1	s__Gluconobacter cerevisiae	85.2402	673	972	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,850] [INFO] GTDB search result was written to GCF_006539125.1_ASM653912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:20,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:20,854] [INFO] DFAST_QC result json was written to GCF_006539125.1_ASM653912v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:20,855] [INFO] DFAST_QC completed!
[2024-01-24 13:02:20,855] [INFO] Total running time: 0h1m0s