[2024-01-24 14:15:02,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,539] [INFO] DQC Reference Directory: /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference
[2024-01-24 14:15:04,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,008] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg17871eb2-0343-47fd-84d4-91b6e4fb60eb/GCF_025995055.1_ASM2599505v1_genomic.fna.gz | prodigal -d GCF_025995055.1_ASM2599505v1_genomic.fna/cds.fna -a GCF_025995055.1_ASM2599505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:13,676] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:13,677] [INFO] Task started: HMMsearch
[2024-01-24 14:15:13,677] [INFO] Running command: hmmsearch --tblout GCF_025995055.1_ASM2599505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/reference_markers.hmm GCF_025995055.1_ASM2599505v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:13,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:13,954] [INFO] Found 6/6 markers.
[2024-01-24 14:15:13,987] [INFO] Query marker FASTA was written to GCF_025995055.1_ASM2599505v1_genomic.fna/markers.fasta
[2024-01-24 14:15:13,987] [INFO] Task started: Blastn
[2024-01-24 14:15:13,987] [INFO] Running command: blastn -query GCF_025995055.1_ASM2599505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/reference_markers.fasta -out GCF_025995055.1_ASM2599505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:14,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:14,799] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:14,799] [INFO] Target genome list was writen to GCF_025995055.1_ASM2599505v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:14,814] [INFO] Task started: fastANI
[2024-01-24 14:15:14,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg17871eb2-0343-47fd-84d4-91b6e4fb60eb/GCF_025995055.1_ASM2599505v1_genomic.fna.gz --refList GCF_025995055.1_ASM2599505v1_genomic.fna/target_genomes.txt --output GCF_025995055.1_ASM2599505v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:22,754] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:22,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:22,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:22,768] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:22,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:22,768] [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 kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	99.9537	964	974	95	conclusive
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	93.8633	846	974	95	below_threshold
Gluconobacter cerevisiae	strain=LMG 27748	GCA_015244675.1	1379734	1379734	type	True	91.3457	815	974	95	below_threshold
Gluconobacter cerevisiae	strain=DSM 27644	GCA_018811965.1	1379734	1379734	type	True	91.3005	810	974	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	90.6832	811	974	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	86.3748	709	974	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	86.1337	714	974	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	85.916	681	974	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	85.7335	722	974	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.7186	166	974	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	77.3095	125	974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,770] [INFO] DFAST Taxonomy check result was written to GCF_025995055.1_ASM2599505v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:22,770] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:22,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:22,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/checkm_data
[2024-01-24 14:15:22,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:22,807] [INFO] Task started: CheckM
[2024-01-24 14:15:22,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995055.1_ASM2599505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995055.1_ASM2599505v1_genomic.fna/checkm_input GCF_025995055.1_ASM2599505v1_genomic.fna/checkm_result
[2024-01-24 14:15:55,023] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:55,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:55,043] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:55,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:55,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995055.1_ASM2599505v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:55,044] [INFO] Task started: Blastn
[2024-01-24 14:15:55,044] [INFO] Running command: blastn -query GCF_025995055.1_ASM2599505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8007c20-fc96-42ef-a0ab-989926c78c2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995055.1_ASM2599505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:56,207] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:56,210] [INFO] Selected 9 target genomes.
[2024-01-24 14:15:56,210] [INFO] Target genome list was writen to GCF_025995055.1_ASM2599505v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:56,232] [INFO] Task started: fastANI
[2024-01-24 14:15:56,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg17871eb2-0343-47fd-84d4-91b6e4fb60eb/GCF_025995055.1_ASM2599505v1_genomic.fna.gz --refList GCF_025995055.1_ASM2599505v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995055.1_ASM2599505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:02,766] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:02,775] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:02,775] [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_002723995.1	s__Gluconobacter kondonii	99.9537	964	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	conclusive
GCF_015244745.1	s__Gluconobacter cadivus	93.8633	846	974	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	91.3457	815	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002723915.1	s__Gluconobacter albidus	90.6832	811	974	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	86.4371	738	974	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	86.3748	709	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	85.9054	682	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_006539125.1	s__Gluconobacter sphaericus	85.9004	698	974	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	85.6569	722	974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:02,776] [INFO] GTDB search result was written to GCF_025995055.1_ASM2599505v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:02,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:02,782] [INFO] DFAST_QC result json was written to GCF_025995055.1_ASM2599505v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:02,782] [INFO] DFAST_QC completed!
[2024-01-24 14:16:02,782] [INFO] Total running time: 0h1m0s