[2024-01-24 11:34:53,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:53,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:53,397] [INFO] DQC Reference Directory: /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference
[2024-01-24 11:34:55,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,643] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f06c1e4-6fc7-4ad7-8c6c-253849c63af3/GCF_018390645.1_ASM1839064v1_genomic.fna.gz | prodigal -d GCF_018390645.1_ASM1839064v1_genomic.fna/cds.fna -a GCF_018390645.1_ASM1839064v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:10,535] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:10,535] [INFO] Task started: HMMsearch
[2024-01-24 11:35:10,535] [INFO] Running command: hmmsearch --tblout GCF_018390645.1_ASM1839064v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/reference_markers.hmm GCF_018390645.1_ASM1839064v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:10,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:10,840] [INFO] Found 6/6 markers.
[2024-01-24 11:35:10,884] [INFO] Query marker FASTA was written to GCF_018390645.1_ASM1839064v1_genomic.fna/markers.fasta
[2024-01-24 11:35:10,885] [INFO] Task started: Blastn
[2024-01-24 11:35:10,885] [INFO] Running command: blastn -query GCF_018390645.1_ASM1839064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/reference_markers.fasta -out GCF_018390645.1_ASM1839064v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:12,027] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:12,030] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:12,030] [INFO] Target genome list was writen to GCF_018390645.1_ASM1839064v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:12,034] [INFO] Task started: fastANI
[2024-01-24 11:35:12,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f06c1e4-6fc7-4ad7-8c6c-253849c63af3/GCF_018390645.1_ASM1839064v1_genomic.fna.gz --refList GCF_018390645.1_ASM1839064v1_genomic.fna/target_genomes.txt --output GCF_018390645.1_ASM1839064v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:23,020] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:23,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:23,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:23,032] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:23,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:23,033] [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
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	100.0	1658	1662	95	conclusive
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	88.5874	1160	1662	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	88.2142	1167	1662	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	86.4848	1010	1662	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	85.8706	1066	1662	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.8982	979	1662	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	78.954	591	1662	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	78.8451	617	1662	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.7991	479	1662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:23,035] [INFO] DFAST Taxonomy check result was written to GCF_018390645.1_ASM1839064v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:23,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:23,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:23,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/checkm_data
[2024-01-24 11:35:23,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:23,085] [INFO] Task started: CheckM
[2024-01-24 11:35:23,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018390645.1_ASM1839064v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018390645.1_ASM1839064v1_genomic.fna/checkm_input GCF_018390645.1_ASM1839064v1_genomic.fna/checkm_result
[2024-01-24 11:36:10,158] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:10,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:10,185] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:10,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:10,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018390645.1_ASM1839064v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:10,187] [INFO] Task started: Blastn
[2024-01-24 11:36:10,187] [INFO] Running command: blastn -query GCF_018390645.1_ASM1839064v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga717e4bb-2466-435a-8dfe-72e24301e022/dqc_reference/reference_markers_gtdb.fasta -out GCF_018390645.1_ASM1839064v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:12,481] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:12,484] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:12,484] [INFO] Target genome list was writen to GCF_018390645.1_ASM1839064v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:12,491] [INFO] Task started: fastANI
[2024-01-24 11:36:12,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f06c1e4-6fc7-4ad7-8c6c-253849c63af3/GCF_018390645.1_ASM1839064v1_genomic.fna.gz --refList GCF_018390645.1_ASM1839064v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018390645.1_ASM1839064v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:22,251] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:22,270] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:22,271] [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_018390645.1	s__Ancylobacter dichloromethanicus	100.0	1658	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100155.1	s__Ancylobacter rudongensis	88.5676	1162	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCA_000378025.1	s__Ancylobacter sp000378025	88.2433	1175	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	88.2298	1165	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.576	1032	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	85.8427	1068	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	85.7865	970	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_017872635.1	s__Starkeya sp017872635	85.7608	1002	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:22,276] [INFO] GTDB search result was written to GCF_018390645.1_ASM1839064v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:22,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:22,282] [INFO] DFAST_QC result json was written to GCF_018390645.1_ASM1839064v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:22,282] [INFO] DFAST_QC completed!
[2024-01-24 11:36:22,283] [INFO] Total running time: 0h1m29s