[2024-01-24 13:13:33,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:33,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:33,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference
[2024-01-24 13:13:34,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:34,670] [INFO] Task started: Prodigal
[2024-01-24 13:13:34,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg69d8d035-0742-437a-8f64-c2e4db0bb857/GCF_026343945.1_ASM2634394v1_genomic.fna.gz | prodigal -d GCF_026343945.1_ASM2634394v1_genomic.fna/cds.fna -a GCF_026343945.1_ASM2634394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:49,998] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:49,998] [INFO] Task started: HMMsearch
[2024-01-24 13:13:49,999] [INFO] Running command: hmmsearch --tblout GCF_026343945.1_ASM2634394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/reference_markers.hmm GCF_026343945.1_ASM2634394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:50,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:50,283] [INFO] Found 6/6 markers.
[2024-01-24 13:13:50,328] [INFO] Query marker FASTA was written to GCF_026343945.1_ASM2634394v1_genomic.fna/markers.fasta
[2024-01-24 13:13:50,328] [INFO] Task started: Blastn
[2024-01-24 13:13:50,328] [INFO] Running command: blastn -query GCF_026343945.1_ASM2634394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/reference_markers.fasta -out GCF_026343945.1_ASM2634394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,331] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:51,331] [INFO] Target genome list was writen to GCF_026343945.1_ASM2634394v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:51,338] [INFO] Task started: fastANI
[2024-01-24 13:13:51,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d8d035-0742-437a-8f64-c2e4db0bb857/GCF_026343945.1_ASM2634394v1_genomic.fna.gz --refList GCF_026343945.1_ASM2634394v1_genomic.fna/target_genomes.txt --output GCF_026343945.1_ASM2634394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:10,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:10,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:10,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:10,680] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:10,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:10,680] [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
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	84.0536	1220	1746	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	80.9452	793	1746	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	80.9065	838	1746	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	80.5799	781	1746	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.6926	444	1746	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	77.5499	385	1746	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.5202	467	1746	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.5143	388	1746	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.4904	275	1746	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	77.2375	325	1746	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	77.2082	328	1746	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	77.1914	334	1746	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	77.1765	332	1746	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.1006	387	1746	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	77.0567	292	1746	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.0229	203	1746	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.8929	318	1746	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.7768	317	1746	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.7406	280	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:10,682] [INFO] DFAST Taxonomy check result was written to GCF_026343945.1_ASM2634394v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:10,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:10,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:10,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/checkm_data
[2024-01-24 13:14:10,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:10,733] [INFO] Task started: CheckM
[2024-01-24 13:14:10,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026343945.1_ASM2634394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026343945.1_ASM2634394v1_genomic.fna/checkm_input GCF_026343945.1_ASM2634394v1_genomic.fna/checkm_result
[2024-01-24 13:14:55,105] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:55,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:55,124] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:55,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:55,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026343945.1_ASM2634394v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:55,125] [INFO] Task started: Blastn
[2024-01-24 13:14:55,125] [INFO] Running command: blastn -query GCF_026343945.1_ASM2634394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d6f105-72fd-4376-8814-9d9ff5544f42/dqc_reference/reference_markers_gtdb.fasta -out GCF_026343945.1_ASM2634394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:56,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:56,828] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:56,829] [INFO] Target genome list was writen to GCF_026343945.1_ASM2634394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:56,858] [INFO] Task started: fastANI
[2024-01-24 13:14:56,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d8d035-0742-437a-8f64-c2e4db0bb857/GCF_026343945.1_ASM2634394v1_genomic.fna.gz --refList GCF_026343945.1_ASM2634394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026343945.1_ASM2634394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:09,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:09,033] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:15:09,033] [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_014196455.1	s__Kaistia hirudinis	84.0535	1220	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCA_017307955.1	s__Kaistia sp017307955	81.4922	885	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	80.9402	794	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	80.8882	840	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	80.8454	811	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	80.5919	588	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	80.58	781	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	77.5341	372	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008365.1	s__Rhizobium leguminosarum	77.2165	327	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	-
GCF_003046175.1	s__Bosea sp003046175	77.0757	341	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949865.1	s__Agrobacterium nepotum	76.3679	219	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002919265.1	s__ZC4RG25 sp002919265	76.1566	83	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	99.72	99.72	0.95	0.95	2	-
GCF_000834635.1	s__Agrobacterium tumefaciens_C	75.9494	89	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.02	95.99	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:09,035] [INFO] GTDB search result was written to GCF_026343945.1_ASM2634394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:09,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:09,039] [INFO] DFAST_QC result json was written to GCF_026343945.1_ASM2634394v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:09,039] [INFO] DFAST_QC completed!
[2024-01-24 13:15:09,039] [INFO] Total running time: 0h1m36s