[2024-01-24 13:25:30,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference
[2024-01-24 13:25:31,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,378] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,378] [INFO] Running command: gunzip -c /var/lib/cwl/stgc32c3c77-71c1-4d22-a160-0c795e426496/GCF_022760995.1_ASM2276099v1_genomic.fna.gz | prodigal -d GCF_022760995.1_ASM2276099v1_genomic.fna/cds.fna -a GCF_022760995.1_ASM2276099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:46,508] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:46,508] [INFO] Task started: HMMsearch
[2024-01-24 13:25:46,509] [INFO] Running command: hmmsearch --tblout GCF_022760995.1_ASM2276099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/reference_markers.hmm GCF_022760995.1_ASM2276099v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:46,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:46,782] [INFO] Found 6/6 markers.
[2024-01-24 13:25:46,828] [INFO] Query marker FASTA was written to GCF_022760995.1_ASM2276099v1_genomic.fna/markers.fasta
[2024-01-24 13:25:46,828] [INFO] Task started: Blastn
[2024-01-24 13:25:46,828] [INFO] Running command: blastn -query GCF_022760995.1_ASM2276099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/reference_markers.fasta -out GCF_022760995.1_ASM2276099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,974] [INFO] Selected 10 target genomes.
[2024-01-24 13:25:47,974] [INFO] Target genome list was writen to GCF_022760995.1_ASM2276099v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:47,981] [INFO] Task started: fastANI
[2024-01-24 13:25:47,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32c3c77-71c1-4d22-a160-0c795e426496/GCF_022760995.1_ASM2276099v1_genomic.fna.gz --refList GCF_022760995.1_ASM2276099v1_genomic.fna/target_genomes.txt --output GCF_022760995.1_ASM2276099v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:58,624] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:58,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:58,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:58,636] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:58,636] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:25:58,636] [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	85.4466	967	1428	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	84.8217	976	1428	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	84.7526	854	1428	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	84.7482	788	1428	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	84.4306	968	1428	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	84.3674	975	1428	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	84.2725	805	1428	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	82.4652	702	1428	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.3823	756	1428	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.5284	431	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:58,638] [INFO] DFAST Taxonomy check result was written to GCF_022760995.1_ASM2276099v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:58,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:58,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:58,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/checkm_data
[2024-01-24 13:25:58,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:58,689] [INFO] Task started: CheckM
[2024-01-24 13:25:58,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022760995.1_ASM2276099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022760995.1_ASM2276099v1_genomic.fna/checkm_input GCF_022760995.1_ASM2276099v1_genomic.fna/checkm_result
[2024-01-24 13:26:47,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:47,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:47,073] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:47,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:47,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022760995.1_ASM2276099v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:47,074] [INFO] Task started: Blastn
[2024-01-24 13:26:47,075] [INFO] Running command: blastn -query GCF_022760995.1_ASM2276099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22d7e5c4-5d66-46b3-97ad-eddf41f0d142/dqc_reference/reference_markers_gtdb.fasta -out GCF_022760995.1_ASM2276099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:49,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:49,220] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:49,220] [INFO] Target genome list was writen to GCF_022760995.1_ASM2276099v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:49,239] [INFO] Task started: fastANI
[2024-01-24 13:26:49,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32c3c77-71c1-4d22-a160-0c795e426496/GCF_022760995.1_ASM2276099v1_genomic.fna.gz --refList GCF_022760995.1_ASM2276099v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022760995.1_ASM2276099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:01,342] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:01,358] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:27:01,359] [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	86.0252	990	1428	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	85.4718	983	1428	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	85.4466	967	1428	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	85.3924	1018	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003264855.1	s__Dyella jiangningensis_C	85.0522	990	1428	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	84.8053	978	1428	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	84.7402	968	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000632805.1	s__Dyella jiangningensis	84.4756	985	1428	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	84.3776	974	1428	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	84.3153	888	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_900112865.1	s__Dyella marensis	84.2503	875	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:01,360] [INFO] GTDB search result was written to GCF_022760995.1_ASM2276099v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:01,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:01,364] [INFO] DFAST_QC result json was written to GCF_022760995.1_ASM2276099v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:01,364] [INFO] DFAST_QC completed!
[2024-01-24 13:27:01,364] [INFO] Total running time: 0h1m31s