[2024-01-24 11:05:34,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference
[2024-01-24 11:05:36,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:36,037] [INFO] Task started: Prodigal
[2024-01-24 11:05:36,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg314cc0b1-c227-4035-98bc-9f14baad2f8d/GCF_016031635.1_ASM1603163v1_genomic.fna.gz | prodigal -d GCF_016031635.1_ASM1603163v1_genomic.fna/cds.fna -a GCF_016031635.1_ASM1603163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:00,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:00,766] [INFO] Task started: HMMsearch
[2024-01-24 11:06:00,766] [INFO] Running command: hmmsearch --tblout GCF_016031635.1_ASM1603163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/reference_markers.hmm GCF_016031635.1_ASM1603163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:01,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:01,222] [INFO] Found 6/6 markers.
[2024-01-24 11:06:01,290] [INFO] Query marker FASTA was written to GCF_016031635.1_ASM1603163v1_genomic.fna/markers.fasta
[2024-01-24 11:06:01,291] [INFO] Task started: Blastn
[2024-01-24 11:06:01,291] [INFO] Running command: blastn -query GCF_016031635.1_ASM1603163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/reference_markers.fasta -out GCF_016031635.1_ASM1603163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:02,386] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:02,487] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:02,487] [INFO] Target genome list was writen to GCF_016031635.1_ASM1603163v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:02,498] [INFO] Task started: fastANI
[2024-01-24 11:06:02,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg314cc0b1-c227-4035-98bc-9f14baad2f8d/GCF_016031635.1_ASM1603163v1_genomic.fna.gz --refList GCF_016031635.1_ASM1603163v1_genomic.fna/target_genomes.txt --output GCF_016031635.1_ASM1603163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:43,938] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:43,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:43,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:43,960] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:43,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:43,960] [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
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	100.0	2753	2756	95	conclusive
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	90.8748	1956	2756	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	89.8743	1806	2756	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	89.6077	1939	2756	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.2295	1965	2756	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.1394	1949	2756	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	89.0881	1940	2756	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	88.9343	1938	2756	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	88.9321	1952	2756	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.8914	1911	2756	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.7882	1863	2756	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.7205	1925	2756	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.6797	1913	2756	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	88.512	1923	2756	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	88.5066	1942	2756	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.2534	1700	2756	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	88.0209	1846	2756	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.7289	1439	2756	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.585	1385	2756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,962] [INFO] DFAST Taxonomy check result was written to GCF_016031635.1_ASM1603163v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:43,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:43,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:43,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/checkm_data
[2024-01-24 11:06:43,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:44,044] [INFO] Task started: CheckM
[2024-01-24 11:06:44,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016031635.1_ASM1603163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016031635.1_ASM1603163v1_genomic.fna/checkm_input GCF_016031635.1_ASM1603163v1_genomic.fna/checkm_result
[2024-01-24 11:07:57,661] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:57,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:57,687] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:57,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:57,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016031635.1_ASM1603163v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:57,688] [INFO] Task started: Blastn
[2024-01-24 11:07:57,689] [INFO] Running command: blastn -query GCF_016031635.1_ASM1603163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a845c65-8a19-44a4-8b34-b1040ab96faa/dqc_reference/reference_markers_gtdb.fasta -out GCF_016031635.1_ASM1603163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:59,938] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:59,942] [INFO] Selected 15 target genomes.
[2024-01-24 11:07:59,942] [INFO] Target genome list was writen to GCF_016031635.1_ASM1603163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:59,955] [INFO] Task started: fastANI
[2024-01-24 11:07:59,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg314cc0b1-c227-4035-98bc-9f14baad2f8d/GCF_016031635.1_ASM1603163v1_genomic.fna.gz --refList GCF_016031635.1_ASM1603163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016031635.1_ASM1603163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:32,687] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:32,706] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:32,706] [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_016031635.1	s__Bradyrhizobium diversitatis	100.0	2753	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	conclusive
GCF_015291725.1	s__Bradyrhizobium japonicum_D	95.1974	2186	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	93.1504	2014	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	91.3844	1980	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000261685.1	s__Bradyrhizobium sp000261685	91.352	1788	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795245.1	s__Bradyrhizobium forestalis	90.8916	1954	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	90.1907	1910	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	90.0914	1939	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570865.1	s__Bradyrhizobium frederickii	89.6029	1940	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	89.2972	1840	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	89.0936	1929	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	89.0435	1905	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	89.0117	1824	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	88.8913	1911	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	87.2629	1761	2756	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:32,708] [INFO] GTDB search result was written to GCF_016031635.1_ASM1603163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:32,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:32,712] [INFO] DFAST_QC result json was written to GCF_016031635.1_ASM1603163v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:32,712] [INFO] DFAST_QC completed!
[2024-01-24 11:08:32,712] [INFO] Total running time: 0h2m58s