[2024-01-25 20:12:20,712] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference
[2024-01-25 20:12:21,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:21,890] [INFO] Task started: Prodigal
[2024-01-25 20:12:21,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea45696-b5fa-4b01-9a9b-14991bcc4231/GCF_001010355.1_ASM101035v1_genomic.fna.gz | prodigal -d GCF_001010355.1_ASM101035v1_genomic.fna/cds.fna -a GCF_001010355.1_ASM101035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:34,173] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:34,173] [INFO] Task started: HMMsearch
[2024-01-25 20:12:34,173] [INFO] Running command: hmmsearch --tblout GCF_001010355.1_ASM101035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/reference_markers.hmm GCF_001010355.1_ASM101035v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:34,391] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:34,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ea45696-b5fa-4b01-9a9b-14991bcc4231/GCF_001010355.1_ASM101035v1_genomic.fna.gz]
[2024-01-25 20:12:34,427] [INFO] Query marker FASTA was written to GCF_001010355.1_ASM101035v1_genomic.fna/markers.fasta
[2024-01-25 20:12:34,428] [INFO] Task started: Blastn
[2024-01-25 20:12:34,428] [INFO] Running command: blastn -query GCF_001010355.1_ASM101035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/reference_markers.fasta -out GCF_001010355.1_ASM101035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:35,252] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:35,258] [INFO] Selected 8 target genomes.
[2024-01-25 20:12:35,259] [INFO] Target genome list was writen to GCF_001010355.1_ASM101035v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:35,270] [INFO] Task started: fastANI
[2024-01-25 20:12:35,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea45696-b5fa-4b01-9a9b-14991bcc4231/GCF_001010355.1_ASM101035v1_genomic.fna.gz --refList GCF_001010355.1_ASM101035v1_genomic.fna/target_genomes.txt --output GCF_001010355.1_ASM101035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:44,094] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:44,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:44,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:44,101] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:44,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:44,102] [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 japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	100.0	1350	1351	95	conclusive
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	87.6888	1062	1351	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	85.0713	952	1351	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	83.8633	812	1351	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	83.8326	860	1351	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.8874	518	1351	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.7347	626	1351	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.0096	296	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:44,103] [INFO] DFAST Taxonomy check result was written to GCF_001010355.1_ASM101035v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:44,103] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:44,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:44,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/checkm_data
[2024-01-25 20:12:44,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:44,147] [INFO] Task started: CheckM
[2024-01-25 20:12:44,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001010355.1_ASM101035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001010355.1_ASM101035v1_genomic.fna/checkm_input GCF_001010355.1_ASM101035v1_genomic.fna/checkm_result
[2024-01-25 20:13:29,590] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:29,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:29,609] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:29,609] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:29,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001010355.1_ASM101035v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:29,610] [INFO] Task started: Blastn
[2024-01-25 20:13:29,611] [INFO] Running command: blastn -query GCF_001010355.1_ASM101035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg474c956d-190e-4822-bc6a-9f1915b1da5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001010355.1_ASM101035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:30,958] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:30,961] [INFO] Selected 10 target genomes.
[2024-01-25 20:13:30,961] [INFO] Target genome list was writen to GCF_001010355.1_ASM101035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:30,967] [INFO] Task started: fastANI
[2024-01-25 20:13:30,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea45696-b5fa-4b01-9a9b-14991bcc4231/GCF_001010355.1_ASM101035v1_genomic.fna.gz --refList GCF_001010355.1_ASM101035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001010355.1_ASM101035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:43,326] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:43,333] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:43,333] [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_001010355.1	s__Dyella japonica	100.0	1350	1351	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_003688835.1	s__Dyella sp003688835	91.2304	1129	1351	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	87.6767	1062	1351	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	85.7188	946	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000725385.1	s__Dyella japonica_C	85.2467	917	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014297575.1	s__Dyella sp014297575	85.0673	953	1351	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	85.0494	934	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878475.1	s__Dyella sp002878475	83.9719	886	1351	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	83.8767	844	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428905.1	s__Dyella sp016428905	83.7903	833	1351	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:43,336] [INFO] GTDB search result was written to GCF_001010355.1_ASM101035v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:43,337] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:43,339] [INFO] DFAST_QC result json was written to GCF_001010355.1_ASM101035v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:43,339] [INFO] DFAST_QC completed!
[2024-01-25 20:13:43,340] [INFO] Total running time: 0h1m23s