[2024-01-25 20:18:20,751] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:20,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:20,753] [INFO] DQC Reference Directory: /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference
[2024-01-25 20:18:22,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,059] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg21722ca8-bc25-45b5-8973-abb05d9ca37a/GCF_026283925.1_ASM2628392v1_genomic.fna.gz | prodigal -d GCF_026283925.1_ASM2628392v1_genomic.fna/cds.fna -a GCF_026283925.1_ASM2628392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:36,392] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:36,392] [INFO] Task started: HMMsearch
[2024-01-25 20:18:36,392] [INFO] Running command: hmmsearch --tblout GCF_026283925.1_ASM2628392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/reference_markers.hmm GCF_026283925.1_ASM2628392v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:36,669] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:36,671] [INFO] Found 6/6 markers.
[2024-01-25 20:18:36,714] [INFO] Query marker FASTA was written to GCF_026283925.1_ASM2628392v1_genomic.fna/markers.fasta
[2024-01-25 20:18:36,715] [INFO] Task started: Blastn
[2024-01-25 20:18:36,715] [INFO] Running command: blastn -query GCF_026283925.1_ASM2628392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/reference_markers.fasta -out GCF_026283925.1_ASM2628392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:37,594] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:37,597] [INFO] Selected 9 target genomes.
[2024-01-25 20:18:37,597] [INFO] Target genome list was writen to GCF_026283925.1_ASM2628392v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:37,608] [INFO] Task started: fastANI
[2024-01-25 20:18:37,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg21722ca8-bc25-45b5-8973-abb05d9ca37a/GCF_026283925.1_ASM2628392v1_genomic.fna.gz --refList GCF_026283925.1_ASM2628392v1_genomic.fna/target_genomes.txt --output GCF_026283925.1_ASM2628392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:46,687] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:46,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:46,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:46,695] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:46,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:46,696] [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
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	83.2757	985	1551	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	83.0686	946	1551	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	82.9792	783	1551	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	82.8463	959	1551	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	82.8159	926	1551	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	81.4618	669	1551	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.905	593	1551	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.6462	683	1551	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.0963	359	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:46,697] [INFO] DFAST Taxonomy check result was written to GCF_026283925.1_ASM2628392v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:46,698] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:46,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:46,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/checkm_data
[2024-01-25 20:18:46,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:46,745] [INFO] Task started: CheckM
[2024-01-25 20:18:46,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026283925.1_ASM2628392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026283925.1_ASM2628392v1_genomic.fna/checkm_input GCF_026283925.1_ASM2628392v1_genomic.fna/checkm_result
[2024-01-25 20:19:32,434] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:32,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:32,453] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:32,453] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:32,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026283925.1_ASM2628392v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:32,454] [INFO] Task started: Blastn
[2024-01-25 20:19:32,454] [INFO] Running command: blastn -query GCF_026283925.1_ASM2628392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee510b2c-a28c-4c73-af6b-8f0998c3c911/dqc_reference/reference_markers_gtdb.fasta -out GCF_026283925.1_ASM2628392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:34,116] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:34,119] [INFO] Selected 14 target genomes.
[2024-01-25 20:19:34,119] [INFO] Target genome list was writen to GCF_026283925.1_ASM2628392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:34,140] [INFO] Task started: fastANI
[2024-01-25 20:19:34,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg21722ca8-bc25-45b5-8973-abb05d9ca37a/GCF_026283925.1_ASM2628392v1_genomic.fna.gz --refList GCF_026283925.1_ASM2628392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026283925.1_ASM2628392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:48,549] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:48,558] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:19:48,558] [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_003332825.1	s__Dyella sp003332825	83.5909	929	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	83.3487	947	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003351225.1	s__Dyella solisilvae	83.2738	985	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	83.0905	943	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	82.999	926	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010355.1	s__Dyella japonica	82.9801	782	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264855.1	s__Dyella jiangningensis_C	82.956	953	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	82.842	959	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	82.8165	926	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	82.8071	923	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688835.1	s__Dyella sp003688835	82.713	926	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	82.3063	803	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_018599185.1	s__Rhodanobacter sp018599185	81.2492	683	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	79.4988	482	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:48,560] [INFO] GTDB search result was written to GCF_026283925.1_ASM2628392v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:48,560] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:48,566] [INFO] DFAST_QC result json was written to GCF_026283925.1_ASM2628392v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:48,566] [INFO] DFAST_QC completed!
[2024-01-25 20:19:48,566] [INFO] Total running time: 0h1m28s