[2024-01-25 17:37:35,734] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:35,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:35,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference
[2024-01-25 17:37:36,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:36,909] [INFO] Task started: Prodigal
[2024-01-25 17:37:36,910] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf64b96e-3c80-46f0-b9a9-6d2918ccef46/GCF_002776695.1_ASM277669v1_genomic.fna.gz | prodigal -d GCF_002776695.1_ASM277669v1_genomic.fna/cds.fna -a GCF_002776695.1_ASM277669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:00,525] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:00,525] [INFO] Task started: HMMsearch
[2024-01-25 17:38:00,526] [INFO] Running command: hmmsearch --tblout GCF_002776695.1_ASM277669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/reference_markers.hmm GCF_002776695.1_ASM277669v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:00,824] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:00,825] [INFO] Found 6/6 markers.
[2024-01-25 17:38:00,888] [INFO] Query marker FASTA was written to GCF_002776695.1_ASM277669v1_genomic.fna/markers.fasta
[2024-01-25 17:38:00,888] [INFO] Task started: Blastn
[2024-01-25 17:38:00,888] [INFO] Running command: blastn -query GCF_002776695.1_ASM277669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/reference_markers.fasta -out GCF_002776695.1_ASM277669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:01,960] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:01,963] [INFO] Selected 19 target genomes.
[2024-01-25 17:38:01,964] [INFO] Target genome list was writen to GCF_002776695.1_ASM277669v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:01,989] [INFO] Task started: fastANI
[2024-01-25 17:38:01,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf64b96e-3c80-46f0-b9a9-6d2918ccef46/GCF_002776695.1_ASM277669v1_genomic.fna.gz --refList GCF_002776695.1_ASM277669v1_genomic.fna/target_genomes.txt --output GCF_002776695.1_ASM277669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:48,406] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:48,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:48,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:48,419] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:48,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:48,420] [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 nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	100.0	2724	2726	95	conclusive
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	90.6574	2037	2726	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	90.6421	1947	2726	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	90.5651	1953	2726	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	90.4287	2026	2726	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	90.3847	1990	2726	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.5329	1978	2726	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.307	2008	2726	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.285	2023	2726	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.2139	1931	2726	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	89.1835	2030	2726	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	89.0834	1927	2726	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.0498	1972	2726	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	89.048	1960	2726	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.8769	1878	2726	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.705	1834	2726	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.6707	1847	2726	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9856	1483	2726	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.83	1381	2726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:48,422] [INFO] DFAST Taxonomy check result was written to GCF_002776695.1_ASM277669v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:48,422] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:48,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:48,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/checkm_data
[2024-01-25 17:38:48,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:48,499] [INFO] Task started: CheckM
[2024-01-25 17:38:48,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002776695.1_ASM277669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002776695.1_ASM277669v1_genomic.fna/checkm_input GCF_002776695.1_ASM277669v1_genomic.fna/checkm_result
[2024-01-25 17:40:09,724] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:09,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:09,748] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:09,748] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:09,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002776695.1_ASM277669v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:09,750] [INFO] Task started: Blastn
[2024-01-25 17:40:09,750] [INFO] Running command: blastn -query GCF_002776695.1_ASM277669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769f6dc4-cbf8-481c-8d68-4621834b8843/dqc_reference/reference_markers_gtdb.fasta -out GCF_002776695.1_ASM277669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:12,049] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:12,052] [INFO] Selected 19 target genomes.
[2024-01-25 17:40:12,052] [INFO] Target genome list was writen to GCF_002776695.1_ASM277669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:12,066] [INFO] Task started: fastANI
[2024-01-25 17:40:12,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf64b96e-3c80-46f0-b9a9-6d2918ccef46/GCF_002776695.1_ASM277669v1_genomic.fna.gz --refList GCF_002776695.1_ASM277669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002776695.1_ASM277669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:56,497] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:56,509] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:56,509] [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_002776695.1	s__Bradyrhizobium nitroreducens	100.0	2725	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	conclusive
GCF_002531575.1	s__Bradyrhizobium sp002531575	93.5701	2103	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963435.1	s__Bradyrhizobium sp003963435	90.778	1546	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291745.1	s__Bradyrhizobium sp015291745	90.7297	2023	2726	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	90.699	2119	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278135.2	s__Bradyrhizobium ottawaense	90.6567	2038	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	-
GCF_004114535.1	s__Bradyrhizobium nanningense	90.6483	1946	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	-
GCF_004570865.1	s__Bradyrhizobium frederickii	90.5722	1952	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	90.539	2025	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_900094605.1	s__Bradyrhizobium shewense	90.378	1991	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	90.2409	1935	2726	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	89.8733	1906	2726	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	89.53	1978	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616425.1	s__Bradyrhizobium diazoefficiens_E	89.4078	1686	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.3093	2008	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.2066	1932	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	89.1006	1828	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	88.832	1907	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_015291645.1	s__Bradyrhizobium sp015291645	87.6176	1877	2726	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:56,510] [INFO] GTDB search result was written to GCF_002776695.1_ASM277669v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:56,511] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:56,514] [INFO] DFAST_QC result json was written to GCF_002776695.1_ASM277669v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:56,514] [INFO] DFAST_QC completed!
[2024-01-25 17:40:56,515] [INFO] Total running time: 0h3m21s