[2024-01-25 18:50:20,739] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,741] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference
[2024-01-25 18:50:21,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,862] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,862] [INFO] Running command: gunzip -c /var/lib/cwl/stge7a8cdc7-2af1-4dd0-8b93-d004638ecfc3/GCF_025995115.1_ASM2599511v1_genomic.fna.gz | prodigal -d GCF_025995115.1_ASM2599511v1_genomic.fna/cds.fna -a GCF_025995115.1_ASM2599511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:29,509] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:29,509] [INFO] Task started: HMMsearch
[2024-01-25 18:50:29,509] [INFO] Running command: hmmsearch --tblout GCF_025995115.1_ASM2599511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/reference_markers.hmm GCF_025995115.1_ASM2599511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:29,698] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:29,699] [INFO] Found 6/6 markers.
[2024-01-25 18:50:29,725] [INFO] Query marker FASTA was written to GCF_025995115.1_ASM2599511v1_genomic.fna/markers.fasta
[2024-01-25 18:50:29,725] [INFO] Task started: Blastn
[2024-01-25 18:50:29,726] [INFO] Running command: blastn -query GCF_025995115.1_ASM2599511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/reference_markers.fasta -out GCF_025995115.1_ASM2599511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:30,460] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:30,464] [INFO] Selected 15 target genomes.
[2024-01-25 18:50:30,464] [INFO] Target genome list was writen to GCF_025995115.1_ASM2599511v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:30,478] [INFO] Task started: fastANI
[2024-01-25 18:50:30,478] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a8cdc7-2af1-4dd0-8b93-d004638ecfc3/GCF_025995115.1_ASM2599511v1_genomic.fna.gz --refList GCF_025995115.1_ASM2599511v1_genomic.fna/target_genomes.txt --output GCF_025995115.1_ASM2599511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:40,456] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:40,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:40,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:40,465] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:40,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:40,465] [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	99.9751	985	990	95	conclusive
Gluconobacter sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	99.9473	950	990	95	conclusive
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	90.6636	723	990	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	90.6016	744	990	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	90.552	753	990	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	90.1072	771	990	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	90.0158	785	990	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	89.4133	760	990	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	87.1191	716	990	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	86.6245	693	990	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	86.2549	707	990	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	86.0981	710	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:40,467] [INFO] DFAST Taxonomy check result was written to GCF_025995115.1_ASM2599511v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:40,467] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:40,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:40,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/checkm_data
[2024-01-25 18:50:40,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:40,499] [INFO] Task started: CheckM
[2024-01-25 18:50:40,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995115.1_ASM2599511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995115.1_ASM2599511v1_genomic.fna/checkm_input GCF_025995115.1_ASM2599511v1_genomic.fna/checkm_result
[2024-01-25 18:51:06,956] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:06,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:06,984] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:06,984] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:06,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995115.1_ASM2599511v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:06,985] [INFO] Task started: Blastn
[2024-01-25 18:51:06,985] [INFO] Running command: blastn -query GCF_025995115.1_ASM2599511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2458441-90e7-453b-bdb5-d58b43a601fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995115.1_ASM2599511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:08,300] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:08,303] [INFO] Selected 11 target genomes.
[2024-01-25 18:51:08,304] [INFO] Target genome list was writen to GCF_025995115.1_ASM2599511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:08,315] [INFO] Task started: fastANI
[2024-01-25 18:51:08,315] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a8cdc7-2af1-4dd0-8b93-d004638ecfc3/GCF_025995115.1_ASM2599511v1_genomic.fna.gz --refList GCF_025995115.1_ASM2599511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995115.1_ASM2599511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:16,059] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:16,066] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:16,066] [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	99.9473	950	990	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	90.6714	722	990	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	90.1477	769	990	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	90.0648	804	990	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	89.4133	760	990	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	87.1191	716	990	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	86.5886	695	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_002723995.1	s__Gluconobacter kondonii	86.2661	706	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	-
GCF_007988905.1	s__Gluconobacter kanchanaburiensis	86.2467	669	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015244745.1	s__Gluconobacter cadivus	86.0791	711	990	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	85.3306	683	990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:16,068] [INFO] GTDB search result was written to GCF_025995115.1_ASM2599511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:16,069] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:16,072] [INFO] DFAST_QC result json was written to GCF_025995115.1_ASM2599511v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:16,072] [INFO] DFAST_QC completed!
[2024-01-25 18:51:16,072] [INFO] Total running time: 0h0m55s