[2024-01-24 14:12:47,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference
[2024-01-24 14:12:48,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,542] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ba7e1dc-155a-41b0-b57d-8228647d860a/GCF_014138635.1_ASM1413863v1_genomic.fna.gz | prodigal -d GCF_014138635.1_ASM1413863v1_genomic.fna/cds.fna -a GCF_014138635.1_ASM1413863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:09,105] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:09,106] [INFO] Task started: HMMsearch
[2024-01-24 14:13:09,106] [INFO] Running command: hmmsearch --tblout GCF_014138635.1_ASM1413863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/reference_markers.hmm GCF_014138635.1_ASM1413863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:09,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:09,458] [INFO] Found 6/6 markers.
[2024-01-24 14:13:09,514] [INFO] Query marker FASTA was written to GCF_014138635.1_ASM1413863v1_genomic.fna/markers.fasta
[2024-01-24 14:13:09,515] [INFO] Task started: Blastn
[2024-01-24 14:13:09,515] [INFO] Running command: blastn -query GCF_014138635.1_ASM1413863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/reference_markers.fasta -out GCF_014138635.1_ASM1413863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:10,597] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:10,601] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:10,601] [INFO] Target genome list was writen to GCF_014138635.1_ASM1413863v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:10,607] [INFO] Task started: fastANI
[2024-01-24 14:13:10,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba7e1dc-155a-41b0-b57d-8228647d860a/GCF_014138635.1_ASM1413863v1_genomic.fna.gz --refList GCF_014138635.1_ASM1413863v1_genomic.fna/target_genomes.txt --output GCF_014138635.1_ASM1413863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:25,483] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:25,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:25,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:25,496] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:25,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:25,496] [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
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	100.0	2201	2207	95	conclusive
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	99.9986	2202	2207	95	conclusive
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	91.9006	1650	2207	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	91.8544	1646	2207	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	86.8194	1335	2207	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	86.8185	1297	2207	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.7249	910	2207	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	80.6613	966	2207	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.7484	726	2207	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0049	637	2207	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.8739	634	2207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,498] [INFO] DFAST Taxonomy check result was written to GCF_014138635.1_ASM1413863v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:25,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:25,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:25,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/checkm_data
[2024-01-24 14:13:25,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:25,561] [INFO] Task started: CheckM
[2024-01-24 14:13:25,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138635.1_ASM1413863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138635.1_ASM1413863v1_genomic.fna/checkm_input GCF_014138635.1_ASM1413863v1_genomic.fna/checkm_result
[2024-01-24 14:14:24,894] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:24,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:24,917] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:24,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:24,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138635.1_ASM1413863v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:24,918] [INFO] Task started: Blastn
[2024-01-24 14:14:24,918] [INFO] Running command: blastn -query GCF_014138635.1_ASM1413863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fdc55d3-c611-4b70-b1c7-a7bbf81b604e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138635.1_ASM1413863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:27,187] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:27,190] [INFO] Selected 9 target genomes.
[2024-01-24 14:14:27,190] [INFO] Target genome list was writen to GCF_014138635.1_ASM1413863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:27,196] [INFO] Task started: fastANI
[2024-01-24 14:14:27,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba7e1dc-155a-41b0-b57d-8228647d860a/GCF_014138635.1_ASM1413863v1_genomic.fna.gz --refList GCF_014138635.1_ASM1413863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138635.1_ASM1413863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:40,930] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:40,938] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:40,939] [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_014138625.1	s__Aminobacter ciceronei	99.9986	2202	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.84	97.89	0.89	0.85	7	conclusive
GCF_900445235.1	s__Aminobacter aminovorans	91.8952	1651	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014863355.1	s__Aminobacter carboxidus	89.4817	1656	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
GCF_018555685.1	s__Aminobacter anthyllidis	89.0598	1631	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	86.819	1299	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_014206975.1	s__Aminobacter aganoensis	86.816	1335	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_000372965.1	s__Aminobacter sp000372965	86.0182	1422	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148805.1	s__Aminobacter sp003148805	85.7138	1309	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724355.1	s__Aminobacter sp001724355	84.517	896	2207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:40,940] [INFO] GTDB search result was written to GCF_014138635.1_ASM1413863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:40,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:40,943] [INFO] DFAST_QC result json was written to GCF_014138635.1_ASM1413863v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:40,944] [INFO] DFAST_QC completed!
[2024-01-24 14:14:40,944] [INFO] Total running time: 0h1m54s