[2024-01-24 12:14:48,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference
[2024-01-24 12:14:50,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,146] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg99a6f5f7-552a-4db1-a6e1-7ac9c6473be1/GCF_003350925.1_ASM335092v1_genomic.fna.gz | prodigal -d GCF_003350925.1_ASM335092v1_genomic.fna/cds.fna -a GCF_003350925.1_ASM335092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:11,819] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:11,820] [INFO] Task started: HMMsearch
[2024-01-24 12:15:11,820] [INFO] Running command: hmmsearch --tblout GCF_003350925.1_ASM335092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/reference_markers.hmm GCF_003350925.1_ASM335092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:12,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:12,214] [INFO] Found 6/6 markers.
[2024-01-24 12:15:12,258] [INFO] Query marker FASTA was written to GCF_003350925.1_ASM335092v1_genomic.fna/markers.fasta
[2024-01-24 12:15:12,258] [INFO] Task started: Blastn
[2024-01-24 12:15:12,258] [INFO] Running command: blastn -query GCF_003350925.1_ASM335092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/reference_markers.fasta -out GCF_003350925.1_ASM335092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:13,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:13,166] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:13,166] [INFO] Target genome list was writen to GCF_003350925.1_ASM335092v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:13,172] [INFO] Task started: fastANI
[2024-01-24 12:15:13,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a6f5f7-552a-4db1-a6e1-7ac9c6473be1/GCF_003350925.1_ASM335092v1_genomic.fna.gz --refList GCF_003350925.1_ASM335092v1_genomic.fna/target_genomes.txt --output GCF_003350925.1_ASM335092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:26,400] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:26,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:26,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:26,418] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:26,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:26,419] [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 tabacisoli	strain=L4-6	GCA_003350925.1	2282381	2282381	type	True	100.0	1671	1674	95	conclusive
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.5703	464	1674	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.4208	579	1674	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.3087	549	1674	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	79.3077	561	1674	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.198	560	1674	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	79.1787	509	1674	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	79.0864	518	1674	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.9961	549	1674	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	78.9729	495	1674	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.9083	453	1674	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.9055	463	1674	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.8993	462	1674	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.0492	221	1674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,420] [INFO] DFAST Taxonomy check result was written to GCF_003350925.1_ASM335092v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:26,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:26,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:26,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/checkm_data
[2024-01-24 12:15:26,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:26,480] [INFO] Task started: CheckM
[2024-01-24 12:15:26,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350925.1_ASM335092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350925.1_ASM335092v1_genomic.fna/checkm_input GCF_003350925.1_ASM335092v1_genomic.fna/checkm_result
[2024-01-24 12:16:26,644] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:26,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:26,673] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:26,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:26,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350925.1_ASM335092v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:26,674] [INFO] Task started: Blastn
[2024-01-24 12:16:26,674] [INFO] Running command: blastn -query GCF_003350925.1_ASM335092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66db1305-14ba-40fe-97e5-829ac65e5469/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350925.1_ASM335092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:28,293] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:28,299] [INFO] Selected 22 target genomes.
[2024-01-24 12:16:28,299] [INFO] Target genome list was writen to GCF_003350925.1_ASM335092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:28,315] [INFO] Task started: fastANI
[2024-01-24 12:16:28,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg99a6f5f7-552a-4db1-a6e1-7ac9c6473be1/GCF_003350925.1_ASM335092v1_genomic.fna.gz --refList GCF_003350925.1_ASM335092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350925.1_ASM335092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:48,722] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:48,746] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:48,747] [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_003350925.1	s__Dyella tabacisoli	100.0	1671	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114495.1	s__Dyella sp900114495	79.6502	750	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	79.6479	705	1674	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	79.6204	729	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_001428405.1	s__Frateuria_A sp001428405	79.5885	607	1674	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_001010355.1	s__Dyella japonica	79.5486	466	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001125.1	s__Rhodanobacter sp002001125	79.5191	548	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332825.1	s__Dyella sp003332825	79.3609	580	1674	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	79.3478	568	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	79.322	548	1674	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	79.2619	601	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002001175.1	s__Rhodanobacter sp002001175	79.2526	542	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651895.1	s__Rhodanobacter panaciterrae	79.2219	545	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	79.1856	562	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725385.1	s__Dyella japonica_C	79.1579	589	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016889805.1	s__Rhodanobacter sp001427365	79.1561	537	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	97.01	96.97	0.88	0.88	3	-
GCF_000334915.1	s__Dyella_A ginsengisoli	78.9363	492	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205795.1	s__Rhodanobacter sp014205795	78.9163	502	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329435.1	s__Rhodanobacter sp008329435	78.9155	542	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878475.1	s__Dyella sp002878475	78.8917	542	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	78.8752	406	1674	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_004799035.1	s__Rhodanobacter lindaniclasticus	78.8059	477	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:48,749] [INFO] GTDB search result was written to GCF_003350925.1_ASM335092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:48,749] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:48,753] [INFO] DFAST_QC result json was written to GCF_003350925.1_ASM335092v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:48,753] [INFO] DFAST_QC completed!
[2024-01-24 12:16:48,753] [INFO] Total running time: 0h1m60s