[2024-01-24 13:22:11,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference
[2024-01-24 13:22:13,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,357] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg48353d8a-a817-4c80-90d9-1e9ebb2cd57d/GCF_004570865.1_ASM457086v1_genomic.fna.gz | prodigal -d GCF_004570865.1_ASM457086v1_genomic.fna/cds.fna -a GCF_004570865.1_ASM457086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:35,071] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:35,071] [INFO] Task started: HMMsearch
[2024-01-24 13:22:35,071] [INFO] Running command: hmmsearch --tblout GCF_004570865.1_ASM457086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/reference_markers.hmm GCF_004570865.1_ASM457086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:35,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:35,483] [INFO] Found 6/6 markers.
[2024-01-24 13:22:35,552] [INFO] Query marker FASTA was written to GCF_004570865.1_ASM457086v1_genomic.fna/markers.fasta
[2024-01-24 13:22:35,552] [INFO] Task started: Blastn
[2024-01-24 13:22:35,552] [INFO] Running command: blastn -query GCF_004570865.1_ASM457086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/reference_markers.fasta -out GCF_004570865.1_ASM457086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:36,616] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:36,619] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:36,619] [INFO] Target genome list was writen to GCF_004570865.1_ASM457086v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:36,624] [INFO] Task started: fastANI
[2024-01-24 13:22:36,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg48353d8a-a817-4c80-90d9-1e9ebb2cd57d/GCF_004570865.1_ASM457086v1_genomic.fna.gz --refList GCF_004570865.1_ASM457086v1_genomic.fna/target_genomes.txt --output GCF_004570865.1_ASM457086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:17,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:17,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:17,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:17,796] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:17,796] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:17,797] [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 frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	100.0	2691	2696	95	conclusive
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	92.106	2014	2696	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	90.6386	1942	2696	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	90.5923	1957	2696	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	90.4073	2094	2696	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	90.1923	2104	2696	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.8984	2025	2696	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.6414	2102	2696	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	89.6274	1936	2696	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	89.2487	1956	2696	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	89.1728	1959	2696	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.1236	1970	2696	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	88.8932	2021	2696	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.5963	1976	2696	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.4213	1699	2696	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	87.064	1790	2696	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.0497	1510	2696	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8558	1414	2696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:17,798] [INFO] DFAST Taxonomy check result was written to GCF_004570865.1_ASM457086v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:17,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:17,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:17,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/checkm_data
[2024-01-24 13:23:17,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:17,875] [INFO] Task started: CheckM
[2024-01-24 13:23:17,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004570865.1_ASM457086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004570865.1_ASM457086v1_genomic.fna/checkm_input GCF_004570865.1_ASM457086v1_genomic.fna/checkm_result
[2024-01-24 13:24:24,113] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:24,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:24,127] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:24,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:24,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004570865.1_ASM457086v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:24,128] [INFO] Task started: Blastn
[2024-01-24 13:24:24,128] [INFO] Running command: blastn -query GCF_004570865.1_ASM457086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c59c39-ebfa-42ff-9b17-7c4e425d6bac/dqc_reference/reference_markers_gtdb.fasta -out GCF_004570865.1_ASM457086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:26,382] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:26,384] [INFO] Selected 15 target genomes.
[2024-01-24 13:24:26,385] [INFO] Target genome list was writen to GCF_004570865.1_ASM457086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:26,392] [INFO] Task started: fastANI
[2024-01-24 13:24:26,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg48353d8a-a817-4c80-90d9-1e9ebb2cd57d/GCF_004570865.1_ASM457086v1_genomic.fna.gz --refList GCF_004570865.1_ASM457086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004570865.1_ASM457086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:01,314] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:01,324] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:01,324] [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_004570865.1	s__Bradyrhizobium frederickii	100.0	2691	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	conclusive
GCF_000482425.1	s__Bradyrhizobium japonicum_B	93.6521	1874	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114535.1	s__Bradyrhizobium nanningense	92.099	2015	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	-
GCF_015291745.1	s__Bradyrhizobium sp015291745	91.4907	1965	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	97.81	0.93	0.92	4	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	90.6942	1944	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	90.656	1940	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	90.6186	1874	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	90.5145	2069	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCA_003963435.1	s__Bradyrhizobium sp003963435	90.4245	1473	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	90.4037	1913	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031635.1	s__Bradyrhizobium diversitatis	89.6274	1936	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	89.4464	1948	2696	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	89.3589	2029	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129405.1	s__Bradyrhizobium iriomotense_B	89.1849	1936	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094575.1	s__Bradyrhizobium yuanmingense	88.8875	2022	2696	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	95.91	0.89	0.81	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:01,326] [INFO] GTDB search result was written to GCF_004570865.1_ASM457086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:01,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:01,329] [INFO] DFAST_QC result json was written to GCF_004570865.1_ASM457086v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:01,329] [INFO] DFAST_QC completed!
[2024-01-24 13:25:01,330] [INFO] Total running time: 0h2m50s