[2024-01-24 12:15:03,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference
[2024-01-24 12:15:04,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:04,771] [INFO] Task started: Prodigal
[2024-01-24 12:15:04,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ebb55b-bcae-4ea4-ab8d-a7065eea628b/GCF_015244565.1_ASM1524456v1_genomic.fna.gz | prodigal -d GCF_015244565.1_ASM1524456v1_genomic.fna/cds.fna -a GCF_015244565.1_ASM1524456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:13,807] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:13,807] [INFO] Task started: HMMsearch
[2024-01-24 12:15:13,808] [INFO] Running command: hmmsearch --tblout GCF_015244565.1_ASM1524456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/reference_markers.hmm GCF_015244565.1_ASM1524456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:14,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:14,077] [INFO] Found 6/6 markers.
[2024-01-24 12:15:14,107] [INFO] Query marker FASTA was written to GCF_015244565.1_ASM1524456v1_genomic.fna/markers.fasta
[2024-01-24 12:15:14,107] [INFO] Task started: Blastn
[2024-01-24 12:15:14,107] [INFO] Running command: blastn -query GCF_015244565.1_ASM1524456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/reference_markers.fasta -out GCF_015244565.1_ASM1524456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:14,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:14,868] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:14,868] [INFO] Target genome list was writen to GCF_015244565.1_ASM1524456v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:14,874] [INFO] Task started: fastANI
[2024-01-24 12:15:14,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ebb55b-bcae-4ea4-ab8d-a7065eea628b/GCF_015244565.1_ASM1524456v1_genomic.fna.gz --refList GCF_015244565.1_ASM1524456v1_genomic.fna/target_genomes.txt --output GCF_015244565.1_ASM1524456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:22,245] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:22,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:22,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:22,262] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:22,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:22,263] [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 vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	100.0	1012	1015	95	conclusive
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	93.0482	798	1015	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	90.5776	776	1015	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	90.534	734	1015	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	90.4729	784	1015	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	89.8049	794	1015	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	89.7866	784	1015	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	89.0243	757	1015	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.912	180	1015	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.294	85	1015	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.9705	74	1015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:22,265] [INFO] DFAST Taxonomy check result was written to GCF_015244565.1_ASM1524456v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:22,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:22,266] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:22,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/checkm_data
[2024-01-24 12:15:22,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:22,304] [INFO] Task started: CheckM
[2024-01-24 12:15:22,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015244565.1_ASM1524456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015244565.1_ASM1524456v1_genomic.fna/checkm_input GCF_015244565.1_ASM1524456v1_genomic.fna/checkm_result
[2024-01-24 12:15:53,644] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:53,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:53,669] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:53,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:53,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015244565.1_ASM1524456v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:53,670] [INFO] Task started: Blastn
[2024-01-24 12:15:53,670] [INFO] Running command: blastn -query GCF_015244565.1_ASM1524456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f8477bc-dcc3-4535-a425-00236a563ef1/dqc_reference/reference_markers_gtdb.fasta -out GCF_015244565.1_ASM1524456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:54,843] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:54,848] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:54,849] [INFO] Target genome list was writen to GCF_015244565.1_ASM1524456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:54,857] [INFO] Task started: fastANI
[2024-01-24 12:15:54,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ebb55b-bcae-4ea4-ab8d-a7065eea628b/GCF_015244565.1_ASM1524456v1_genomic.fna.gz --refList GCF_015244565.1_ASM1524456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015244565.1_ASM1524456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:02,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:02,521] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:02,521] [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_015244565.1	s__Gluconobacter vitians	100.0	1012	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006538885.1	s__Gluconobacter roseus	93.0516	798	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006539685.1	s__Gluconobacter oxydans	90.534	734	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_001580675.1	s__Gluconobacter potus	89.7913	784	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_018811945.1	s__Gluconobacter sp018811945	89.4205	779	1015	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	89.0243	757	1015	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	86.2484	760	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_015244745.1	s__Gluconobacter cadivus	85.7989	754	1015	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,523] [INFO] GTDB search result was written to GCF_015244565.1_ASM1524456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:02,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:02,526] [INFO] DFAST_QC result json was written to GCF_015244565.1_ASM1524456v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:02,527] [INFO] DFAST_QC completed!
[2024-01-24 12:16:02,527] [INFO] Total running time: 0h0m59s