[2024-01-24 11:43:38,036] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:38,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:38,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference
[2024-01-24 11:43:39,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:39,257] [INFO] Task started: Prodigal
[2024-01-24 11:43:39,257] [INFO] Running command: gunzip -c /var/lib/cwl/stge40f4137-0953-49f7-a9b6-6aeda75299a1/GCF_014297575.1_ASM1429757v1_genomic.fna.gz | prodigal -d GCF_014297575.1_ASM1429757v1_genomic.fna/cds.fna -a GCF_014297575.1_ASM1429757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,374] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,374] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,374] [INFO] Running command: hmmsearch --tblout GCF_014297575.1_ASM1429757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/reference_markers.hmm GCF_014297575.1_ASM1429757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,777] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,819] [INFO] Query marker FASTA was written to GCF_014297575.1_ASM1429757v1_genomic.fna/markers.fasta
[2024-01-24 11:44:05,819] [INFO] Task started: Blastn
[2024-01-24 11:44:05,819] [INFO] Running command: blastn -query GCF_014297575.1_ASM1429757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/reference_markers.fasta -out GCF_014297575.1_ASM1429757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,928] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,931] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:06,931] [INFO] Target genome list was writen to GCF_014297575.1_ASM1429757v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:06,935] [INFO] Task started: fastANI
[2024-01-24 11:44:06,935] [INFO] Running command: fastANI --query /var/lib/cwl/stge40f4137-0953-49f7-a9b6-6aeda75299a1/GCF_014297575.1_ASM1429757v1_genomic.fna.gz --refList GCF_014297575.1_ASM1429757v1_genomic.fna/target_genomes.txt --output GCF_014297575.1_ASM1429757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:20,323] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:20,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:20,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:20,334] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:20,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:20,335] [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 telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	100.0	1663	1663	95	conclusive
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	85.2426	1125	1663	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	85.054	953	1663	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	84.2776	1084	1663	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	84.1217	1006	1663	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	81.9946	711	1663	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.8639	651	1663	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.5359	747	1663	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.9012	359	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:20,337] [INFO] DFAST Taxonomy check result was written to GCF_014297575.1_ASM1429757v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:20,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:20,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:20,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/checkm_data
[2024-01-24 11:44:20,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:20,407] [INFO] Task started: CheckM
[2024-01-24 11:44:20,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297575.1_ASM1429757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297575.1_ASM1429757v1_genomic.fna/checkm_input GCF_014297575.1_ASM1429757v1_genomic.fna/checkm_result
[2024-01-24 11:45:50,182] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:50,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:50,205] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:50,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:50,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297575.1_ASM1429757v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:50,206] [INFO] Task started: Blastn
[2024-01-24 11:45:50,207] [INFO] Running command: blastn -query GCF_014297575.1_ASM1429757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b779bd9-cf72-47ca-9b9d-1a2e2d20ae83/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297575.1_ASM1429757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:52,142] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:52,147] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:52,148] [INFO] Target genome list was writen to GCF_014297575.1_ASM1429757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:52,157] [INFO] Task started: fastANI
[2024-01-24 11:45:52,157] [INFO] Running command: fastANI --query /var/lib/cwl/stge40f4137-0953-49f7-a9b6-6aeda75299a1/GCF_014297575.1_ASM1429757v1_genomic.fna.gz --refList GCF_014297575.1_ASM1429757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297575.1_ASM1429757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:06,701] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:06,714] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:06,714] [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_014297575.1	s__Dyella sp014297575	100.0	1663	1663	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_000725385.1	s__Dyella japonica_C	87.0496	1240	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201105.1	s__Dyella jiangningensis_B	86.732	1231	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016905005.1	s__Dyella kyungheensis	85.2156	1128	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	85.1139	1115	1663	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	85.0627	952	1663	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	84.9925	1113	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332825.1	s__Dyella sp003332825	84.451	1015	1663	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	84.2775	1084	1663	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	84.1818	1045	1663	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	84.0885	1010	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:06,716] [INFO] GTDB search result was written to GCF_014297575.1_ASM1429757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:06,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:06,719] [INFO] DFAST_QC result json was written to GCF_014297575.1_ASM1429757v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:06,719] [INFO] DFAST_QC completed!
[2024-01-24 11:46:06,719] [INFO] Total running time: 0h2m29s