[2024-01-24 12:36:24,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference
[2024-01-24 12:36:26,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,013] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,014] [INFO] Running command: gunzip -c /var/lib/cwl/stga9ca661b-aebd-4db9-a2be-e0bf55bc664f/GCF_000761445.1_ASM76144v1_genomic.fna.gz | prodigal -d GCF_000761445.1_ASM76144v1_genomic.fna/cds.fna -a GCF_000761445.1_ASM76144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:36,642] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:36,642] [INFO] Task started: HMMsearch
[2024-01-24 12:36:36,642] [INFO] Running command: hmmsearch --tblout GCF_000761445.1_ASM76144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/reference_markers.hmm GCF_000761445.1_ASM76144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:36,948] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:36,949] [INFO] Found 6/6 markers.
[2024-01-24 12:36:36,985] [INFO] Query marker FASTA was written to GCF_000761445.1_ASM76144v1_genomic.fna/markers.fasta
[2024-01-24 12:36:36,985] [INFO] Task started: Blastn
[2024-01-24 12:36:36,985] [INFO] Running command: blastn -query GCF_000761445.1_ASM76144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/reference_markers.fasta -out GCF_000761445.1_ASM76144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:38,019] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:38,023] [INFO] Selected 11 target genomes.
[2024-01-24 12:36:38,023] [INFO] Target genome list was writen to GCF_000761445.1_ASM76144v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:38,028] [INFO] Task started: fastANI
[2024-01-24 12:36:38,028] [INFO] Running command: fastANI --query /var/lib/cwl/stga9ca661b-aebd-4db9-a2be-e0bf55bc664f/GCF_000761445.1_ASM76144v1_genomic.fna.gz --refList GCF_000761445.1_ASM76144v1_genomic.fna/target_genomes.txt --output GCF_000761445.1_ASM76144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:47,165] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:47,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:47,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:47,178] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:36:47,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:47,178] [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
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	100.0	1121	1123	95	conclusive
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	99.9908	1120	1123	95	conclusive
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	87.6609	895	1123	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	81.0862	621	1123	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.9655	589	1123	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.1236	550	1123	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.8316	510	1123	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.4724	409	1123	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.4093	504	1123	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	79.2114	495	1123	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.5282	413	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:47,180] [INFO] DFAST Taxonomy check result was written to GCF_000761445.1_ASM76144v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:47,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:47,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:47,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/checkm_data
[2024-01-24 12:36:47,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:47,215] [INFO] Task started: CheckM
[2024-01-24 12:36:47,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000761445.1_ASM76144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000761445.1_ASM76144v1_genomic.fna/checkm_input GCF_000761445.1_ASM76144v1_genomic.fna/checkm_result
[2024-01-24 12:37:28,991] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:28,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:29,012] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:29,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:29,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000761445.1_ASM76144v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:29,013] [INFO] Task started: Blastn
[2024-01-24 12:37:29,013] [INFO] Running command: blastn -query GCF_000761445.1_ASM76144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9351d1-3a8a-4b02-8ffc-15e792529a7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000761445.1_ASM76144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:31,175] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:31,180] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:31,180] [INFO] Target genome list was writen to GCF_000761445.1_ASM76144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:31,196] [INFO] Task started: fastANI
[2024-01-24 12:37:31,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga9ca661b-aebd-4db9-a2be-e0bf55bc664f/GCF_000761445.1_ASM76144v1_genomic.fna.gz --refList GCF_000761445.1_ASM76144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000761445.1_ASM76144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:42,645] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:42,660] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:42,661] [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_000761445.1	s__Oleiagrimonas soli	100.0	1121	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_012395255.1	s__Oleiagrimonas citrea	87.6609	895	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	98.37	98.37	0.90	0.90	2	-
GCF_003148905.1	s__Fulvimonas soli	81.1034	620	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	80.6885	539	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	80.636	557	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	80.5973	576	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	80.5893	601	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	80.5617	617	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	80.5057	620	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012275375.1	s__Dyella sp012275375	80.4401	607	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_011759385.1	s__Oleiagrimonas sp011759385	80.3808	561	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	80.3298	598	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_003332825.1	s__Dyella sp003332825	79.8867	526	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967035.1	s__Aerosticca soli	79.768	447	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Aerosticca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:42,662] [INFO] GTDB search result was written to GCF_000761445.1_ASM76144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:42,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:42,668] [INFO] DFAST_QC result json was written to GCF_000761445.1_ASM76144v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:42,668] [INFO] DFAST_QC completed!
[2024-01-24 12:37:42,668] [INFO] Total running time: 0h1m18s