[2024-01-24 13:31:35,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference
[2024-01-24 13:31:36,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,840] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cb99cb3-ecc4-4282-a7cc-7ad8e8614c0f/GCF_014206975.1_ASM1420697v1_genomic.fna.gz | prodigal -d GCF_014206975.1_ASM1420697v1_genomic.fna/cds.fna -a GCF_014206975.1_ASM1420697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,784] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,784] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,784] [INFO] Running command: hmmsearch --tblout GCF_014206975.1_ASM1420697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/reference_markers.hmm GCF_014206975.1_ASM1420697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:55,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:55,198] [INFO] Found 6/6 markers.
[2024-01-24 13:31:55,262] [INFO] Query marker FASTA was written to GCF_014206975.1_ASM1420697v1_genomic.fna/markers.fasta
[2024-01-24 13:31:55,262] [INFO] Task started: Blastn
[2024-01-24 13:31:55,262] [INFO] Running command: blastn -query GCF_014206975.1_ASM1420697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/reference_markers.fasta -out GCF_014206975.1_ASM1420697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:56,348] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:56,351] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:56,352] [INFO] Target genome list was writen to GCF_014206975.1_ASM1420697v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:56,361] [INFO] Task started: fastANI
[2024-01-24 13:31:56,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb99cb3-ecc4-4282-a7cc-7ad8e8614c0f/GCF_014206975.1_ASM1420697v1_genomic.fna.gz --refList GCF_014206975.1_ASM1420697v1_genomic.fna/target_genomes.txt --output GCF_014206975.1_ASM1420697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:18,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:18,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:18,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:18,637] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:18,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:18,638] [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 aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	100.0	1897	1898	95	conclusive
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	91.0063	1437	1898	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	86.9388	1295	1898	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	86.9326	1282	1898	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	86.9287	1315	1898	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	86.8937	1319	1898	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	81.3475	950	1898	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	81.2012	811	1898	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	81.1188	882	1898	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	81.0943	944	1898	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	80.9383	862	1898	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	80.1383	744	1898	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.5108	682	1898	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.2059	623	1898	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	79.0708	579	1898	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	78.9848	602	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:18,645] [INFO] DFAST Taxonomy check result was written to GCF_014206975.1_ASM1420697v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:18,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:18,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:18,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/checkm_data
[2024-01-24 13:32:18,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:18,710] [INFO] Task started: CheckM
[2024-01-24 13:32:18,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014206975.1_ASM1420697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014206975.1_ASM1420697v1_genomic.fna/checkm_input GCF_014206975.1_ASM1420697v1_genomic.fna/checkm_result
[2024-01-24 13:33:12,498] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:12,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,517] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:12,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:12,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014206975.1_ASM1420697v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:12,518] [INFO] Task started: Blastn
[2024-01-24 13:33:12,518] [INFO] Running command: blastn -query GCF_014206975.1_ASM1420697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6862e5f3-8b44-4a01-b197-dec990aed4d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014206975.1_ASM1420697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,509] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,513] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:14,513] [INFO] Target genome list was writen to GCF_014206975.1_ASM1420697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:14,539] [INFO] Task started: fastANI
[2024-01-24 13:33:14,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb99cb3-ecc4-4282-a7cc-7ad8e8614c0f/GCF_014206975.1_ASM1420697v1_genomic.fna.gz --refList GCF_014206975.1_ASM1420697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014206975.1_ASM1420697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:34,184] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:34,201] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:34,201] [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_014206975.1	s__Aminobacter aganoensis	100.0	1897	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	conclusive
GCF_014200015.1	s__Aminobacter niigataensis	91.0063	1437	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_018555685.1	s__Aminobacter anthyllidis	87.3011	1327	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863355.1	s__Aminobacter carboxidus	86.9519	1342	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900445235.1	s__Aminobacter aminovorans	86.941	1296	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014138625.1	s__Aminobacter ciceronei	86.9402	1314	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.84	97.89	0.89	0.85	7	-
GCF_000372965.1	s__Aminobacter sp000372965	86.1748	1265	1898	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	86.1123	1253	1898	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	85.3478	904	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	81.3401	943	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCA_000824845.1	s__Mesorhizobium sp000824845	81.2139	901	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	81.2049	900	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004017535.1	s__Mesorhizobium sp004017535	81.0949	926	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:34,203] [INFO] GTDB search result was written to GCF_014206975.1_ASM1420697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:34,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:34,207] [INFO] DFAST_QC result json was written to GCF_014206975.1_ASM1420697v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:34,207] [INFO] DFAST_QC completed!
[2024-01-24 13:33:34,207] [INFO] Total running time: 0h1m59s