[2024-01-24 14:11:51,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,197] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,198] [INFO] DQC Reference Directory: /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference
[2024-01-24 14:11:52,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,656] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg20045e20-a044-4156-97cc-77b8dd354c0b/GCF_003010935.1_ASM301093v1_genomic.fna.gz | prodigal -d GCF_003010935.1_ASM301093v1_genomic.fna/cds.fna -a GCF_003010935.1_ASM301093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:10,855] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:10,855] [INFO] Task started: HMMsearch
[2024-01-24 14:12:10,855] [INFO] Running command: hmmsearch --tblout GCF_003010935.1_ASM301093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/reference_markers.hmm GCF_003010935.1_ASM301093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:11,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:11,332] [INFO] Found 6/6 markers.
[2024-01-24 14:12:11,388] [INFO] Query marker FASTA was written to GCF_003010935.1_ASM301093v1_genomic.fna/markers.fasta
[2024-01-24 14:12:11,388] [INFO] Task started: Blastn
[2024-01-24 14:12:11,388] [INFO] Running command: blastn -query GCF_003010935.1_ASM301093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/reference_markers.fasta -out GCF_003010935.1_ASM301093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:12,516] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:12,520] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:12,520] [INFO] Target genome list was writen to GCF_003010935.1_ASM301093v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:12,525] [INFO] Task started: fastANI
[2024-01-24 14:12:12,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg20045e20-a044-4156-97cc-77b8dd354c0b/GCF_003010935.1_ASM301093v1_genomic.fna.gz --refList GCF_003010935.1_ASM301093v1_genomic.fna/target_genomes.txt --output GCF_003010935.1_ASM301093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:26,289] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:26,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:26,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:26,305] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:12:26,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:26,305] [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
Phyllobacterium endophyticum	strain=PEPV15	GCA_003010935.1	1149773	1149773	type	True	100.0	1831	1832	95	conclusive
Phyllobacterium endophyticum	strain=CECT 7949	GCA_014192255.1	1149773	1149773	type	True	99.9973	1828	1832	95	conclusive
Phyllobacterium endophyticum	strain=PEPV15	GCA_008180215.1	1149773	1149773	type	True	99.99	1822	1832	95	conclusive
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	82.7083	1159	1832	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	82.6888	1157	1832	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	77.4312	239	1832	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	77.3638	243	1832	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.2203	243	1832	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.1561	269	1832	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	76.8119	230	1832	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	76.7729	108	1832	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.7711	136	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:26,307] [INFO] DFAST Taxonomy check result was written to GCF_003010935.1_ASM301093v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:26,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:26,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:26,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/checkm_data
[2024-01-24 14:12:26,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:26,371] [INFO] Task started: CheckM
[2024-01-24 14:12:26,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003010935.1_ASM301093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003010935.1_ASM301093v1_genomic.fna/checkm_input GCF_003010935.1_ASM301093v1_genomic.fna/checkm_result
[2024-01-24 14:13:19,740] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:19,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,765] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:19,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:19,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003010935.1_ASM301093v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:19,766] [INFO] Task started: Blastn
[2024-01-24 14:13:19,767] [INFO] Running command: blastn -query GCF_003010935.1_ASM301093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81f6c19-9caf-4c13-8ff8-2891644d3dec/dqc_reference/reference_markers_gtdb.fasta -out GCF_003010935.1_ASM301093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:21,418] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:21,421] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:21,421] [INFO] Target genome list was writen to GCF_003010935.1_ASM301093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:21,429] [INFO] Task started: fastANI
[2024-01-24 14:13:21,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg20045e20-a044-4156-97cc-77b8dd354c0b/GCF_003010935.1_ASM301093v1_genomic.fna.gz --refList GCF_003010935.1_ASM301093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003010935.1_ASM301093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:34,092] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:34,152] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:34,152] [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_003010935.1	s__Phyllobacterium endophyticum	100.0	1831	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.50	98.51	0.95	0.87	4	conclusive
GCF_003337575.1	s__Phyllobacterium bourgognense	82.7016	1160	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192095.1	s__Phyllobacterium trifolii	82.6839	1158	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.32	99.28	0.88	0.88	4	-
GCF_017833775.1	s__Phyllobacterium sp017833775	81.7344	1104	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002764115.1	s__Phyllobacterium zundukense	80.2121	859	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003010965.1	s__Phyllobacterium sophorae	79.7821	840	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.00	98.48	0.92	0.90	3	-
GCF_003010955.1	s__Phyllobacterium brassicacearum	79.7811	780	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000182645.1	s__Ochrobactrum intermedium	77.4312	239	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.99	97.16	0.92	0.84	56	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	77.2114	255	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756615.1	s__DUSC01 sp016756615	76.9423	236	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	98.60	98.60	0.90	0.90	2	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	76.6955	107	1832	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:34,154] [INFO] GTDB search result was written to GCF_003010935.1_ASM301093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:34,154] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:34,157] [INFO] DFAST_QC result json was written to GCF_003010935.1_ASM301093v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:34,157] [INFO] DFAST_QC completed!
[2024-01-24 14:13:34,158] [INFO] Total running time: 0h1m43s