[2024-01-24 10:57:50,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference
[2024-01-24 10:57:52,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,648] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,649] [INFO] Running command: gunzip -c /var/lib/cwl/stgada5aa6a-5de9-4520-8370-19e066618794/GCF_003207855.1_ASM320785v1_genomic.fna.gz | prodigal -d GCF_003207855.1_ASM320785v1_genomic.fna/cds.fna -a GCF_003207855.1_ASM320785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:04,261] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:04,261] [INFO] Task started: HMMsearch
[2024-01-24 10:58:04,261] [INFO] Running command: hmmsearch --tblout GCF_003207855.1_ASM320785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/reference_markers.hmm GCF_003207855.1_ASM320785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:04,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:04,518] [INFO] Found 6/6 markers.
[2024-01-24 10:58:04,559] [INFO] Query marker FASTA was written to GCF_003207855.1_ASM320785v1_genomic.fna/markers.fasta
[2024-01-24 10:58:04,560] [INFO] Task started: Blastn
[2024-01-24 10:58:04,560] [INFO] Running command: blastn -query GCF_003207855.1_ASM320785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/reference_markers.fasta -out GCF_003207855.1_ASM320785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:05,396] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:05,400] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:05,400] [INFO] Target genome list was writen to GCF_003207855.1_ASM320785v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:05,424] [INFO] Task started: fastANI
[2024-01-24 10:58:05,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgada5aa6a-5de9-4520-8370-19e066618794/GCF_003207855.1_ASM320785v1_genomic.fna.gz --refList GCF_003207855.1_ASM320785v1_genomic.fna/target_genomes.txt --output GCF_003207855.1_ASM320785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:18,980] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:18,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:18,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:18,999] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:19,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:19,000] [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
Komagataeibacter rhaeticus	strain=LMG 22126	GCA_003207855.1	215221	215221	type	True	100.0	1127	1127	95	conclusive
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	86.0413	796	1127	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	85.8594	754	1127	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	85.8276	801	1127	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	85.484	783	1127	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	85.365	798	1127	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	85.2901	774	1127	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	85.2752	773	1127	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	85.1428	795	1127	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	84.8081	793	1127	95	below_threshold
Komagataeibacter kakiaceti	strain=JCM 25156	GCA_000613305.1	943261	943261	type	True	84.3117	347	1127	95	below_threshold
Komagataeibacter saccharivorans	strain=LMG 1582	GCA_003207825.1	265959	265959	type	True	84.0747	722	1127	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.2381	358	1127	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.232	115	1127	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1338	52	1127	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.9747	73	1127	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	75.9746	54	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:19,002] [INFO] DFAST Taxonomy check result was written to GCF_003207855.1_ASM320785v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:19,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:19,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:19,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/checkm_data
[2024-01-24 10:58:19,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:19,043] [INFO] Task started: CheckM
[2024-01-24 10:58:19,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003207855.1_ASM320785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003207855.1_ASM320785v1_genomic.fna/checkm_input GCF_003207855.1_ASM320785v1_genomic.fna/checkm_result
[2024-01-24 10:58:56,680] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:56,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:56,703] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:56,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:56,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003207855.1_ASM320785v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:56,705] [INFO] Task started: Blastn
[2024-01-24 10:58:56,705] [INFO] Running command: blastn -query GCF_003207855.1_ASM320785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18edede-6af4-44a3-b0c1-bdb86a72f2c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003207855.1_ASM320785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:58,211] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:58,215] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:58,216] [INFO] Target genome list was writen to GCF_003207855.1_ASM320785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:58,226] [INFO] Task started: fastANI
[2024-01-24 10:58:58,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgada5aa6a-5de9-4520-8370-19e066618794/GCF_003207855.1_ASM320785v1_genomic.fna.gz --refList GCF_003207855.1_ASM320785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003207855.1_ASM320785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:09,697] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:09,721] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:09,721] [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_003207855.1	s__Komagataeibacter rhaeticus	100.0	1127	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	conclusive
GCF_000182745.2	s__Komagataeibacter medellinensis	87.7228	847	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.49	98.49	0.84	0.84	2	-
GCF_003207895.1	s__Komagataeibacter swingsii	86.0272	796	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_000285295.1	s__Komagataeibacter europaeus	85.8388	800	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	85.7476	816	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015155755.1	s__Komagataeibacter sp015155755	85.6029	747	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207815.1	s__Komagataeibacter oboediens	85.3736	797	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	85.3074	772	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207795.1	s__Komagataeibacter nataicola	85.275	773	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	-
GCF_000964425.1	s__Komagataeibacter intermedius	85.1257	797	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	85.1124	794	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538165.1	s__Komagataeibacter diospyri	84.8233	792	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	84.7771	737	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003207825.1	s__Komagataeibacter saccharivorans	84.0882	721	1127	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.47	98.42	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:09,723] [INFO] GTDB search result was written to GCF_003207855.1_ASM320785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:09,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:09,727] [INFO] DFAST_QC result json was written to GCF_003207855.1_ASM320785v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:09,727] [INFO] DFAST_QC completed!
[2024-01-24 10:59:09,727] [INFO] Total running time: 0h1m19s