[2024-01-24 10:47:24,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference
[2024-01-24 10:47:26,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,546] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg8be53d6f-4fd2-4784-b81d-106aa6eb73b4/GCF_030160255.1_ASM3016025v1_genomic.fna.gz | prodigal -d GCF_030160255.1_ASM3016025v1_genomic.fna/cds.fna -a GCF_030160255.1_ASM3016025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:36,510] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:36,510] [INFO] Task started: HMMsearch
[2024-01-24 10:47:36,510] [INFO] Running command: hmmsearch --tblout GCF_030160255.1_ASM3016025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/reference_markers.hmm GCF_030160255.1_ASM3016025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:36,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:36,788] [INFO] Found 6/6 markers.
[2024-01-24 10:47:36,819] [INFO] Query marker FASTA was written to GCF_030160255.1_ASM3016025v1_genomic.fna/markers.fasta
[2024-01-24 10:47:36,820] [INFO] Task started: Blastn
[2024-01-24 10:47:36,820] [INFO] Running command: blastn -query GCF_030160255.1_ASM3016025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/reference_markers.fasta -out GCF_030160255.1_ASM3016025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:37,521] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:37,524] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:37,524] [INFO] Target genome list was writen to GCF_030160255.1_ASM3016025v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,529] [INFO] Task started: fastANI
[2024-01-24 10:47:37,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg8be53d6f-4fd2-4784-b81d-106aa6eb73b4/GCF_030160255.1_ASM3016025v1_genomic.fna.gz --refList GCF_030160255.1_ASM3016025v1_genomic.fna/target_genomes.txt --output GCF_030160255.1_ASM3016025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:48,432] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:48,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:48,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:48,449] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:48,449] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:48,449] [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=LMG1414	GCA_015244605.1	574987	574987	type	True	99.9814	999	1149	95	conclusive
Gluconobacter sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	99.9394	960	1149	95	conclusive
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	90.7377	738	1149	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	90.6897	750	1149	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	90.6413	751	1149	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	90.1492	779	1149	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	90.0642	792	1149	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	89.5281	765	1149	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	87.2993	718	1149	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	86.5869	723	1149	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	86.2941	722	1149	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	86.1879	739	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:48,451] [INFO] DFAST Taxonomy check result was written to GCF_030160255.1_ASM3016025v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:48,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:48,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:48,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/checkm_data
[2024-01-24 10:47:48,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:48,488] [INFO] Task started: CheckM
[2024-01-24 10:47:48,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160255.1_ASM3016025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160255.1_ASM3016025v1_genomic.fna/checkm_input GCF_030160255.1_ASM3016025v1_genomic.fna/checkm_result
[2024-01-24 10:48:22,402] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:22,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 20.83%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,436] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:22,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:22,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160255.1_ASM3016025v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:22,438] [INFO] Task started: Blastn
[2024-01-24 10:48:22,438] [INFO] Running command: blastn -query GCF_030160255.1_ASM3016025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b79fb16-94a3-4743-bcc9-2aa5b2bab52d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160255.1_ASM3016025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:23,477] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:23,480] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:23,480] [INFO] Target genome list was writen to GCF_030160255.1_ASM3016025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:23,488] [INFO] Task started: fastANI
[2024-01-24 10:48:23,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg8be53d6f-4fd2-4784-b81d-106aa6eb73b4/GCF_030160255.1_ASM3016025v1_genomic.fna.gz --refList GCF_030160255.1_ASM3016025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160255.1_ASM3016025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:32,342] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:32,357] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:32,357] [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	99.9394	960	1149	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	90.7377	738	1149	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	90.2196	806	1149	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	90.1492	779	1149	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	89.5262	765	1149	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	87.282	719	1149	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	86.5808	723	1149	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	86.3962	674	1149	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	86.2871	722	1149	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	86.2009	738	1149	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	85.3118	694	1149	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 10:48:32,359] [INFO] GTDB search result was written to GCF_030160255.1_ASM3016025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:32,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:32,362] [INFO] DFAST_QC result json was written to GCF_030160255.1_ASM3016025v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:32,363] [INFO] DFAST_QC completed!
[2024-01-24 10:48:32,363] [INFO] Total running time: 0h1m8s