[2024-01-24 13:31:44,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference
[2024-01-24 13:31:45,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,460] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,461] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0365097-223a-451f-a5d9-65c623b52959/GCF_008123965.1_ASM812396v1_genomic.fna.gz | prodigal -d GCF_008123965.1_ASM812396v1_genomic.fna/cds.fna -a GCF_008123965.1_ASM812396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:10,773] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:10,774] [INFO] Task started: HMMsearch
[2024-01-24 13:32:10,774] [INFO] Running command: hmmsearch --tblout GCF_008123965.1_ASM812396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/reference_markers.hmm GCF_008123965.1_ASM812396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:11,149] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:11,151] [INFO] Found 6/6 markers.
[2024-01-24 13:32:11,224] [INFO] Query marker FASTA was written to GCF_008123965.1_ASM812396v1_genomic.fna/markers.fasta
[2024-01-24 13:32:11,225] [INFO] Task started: Blastn
[2024-01-24 13:32:11,225] [INFO] Running command: blastn -query GCF_008123965.1_ASM812396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/reference_markers.fasta -out GCF_008123965.1_ASM812396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:12,303] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:12,306] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:12,307] [INFO] Target genome list was writen to GCF_008123965.1_ASM812396v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:12,313] [INFO] Task started: fastANI
[2024-01-24 13:32:12,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0365097-223a-451f-a5d9-65c623b52959/GCF_008123965.1_ASM812396v1_genomic.fna.gz --refList GCF_008123965.1_ASM812396v1_genomic.fna/target_genomes.txt --output GCF_008123965.1_ASM812396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:58,296] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:58,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:58,319] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:58,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:58,319] [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 hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	100.0	2775	2790	95	conclusive
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.0536	1937	2790	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	87.7941	1799	2790	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	87.7436	1810	2790	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	87.7411	1838	2790	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	87.7169	1874	2790	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	87.706	1839	2790	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	87.6773	1634	2790	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	87.6765	1637	2790	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	87.4778	1705	2790	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	87.3806	1793	2790	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	87.3557	1759	2790	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	87.3222	1826	2790	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	87.2793	1963	2790	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	87.2772	1829	2790	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	87.2101	1832	2790	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	87.0659	1761	2790	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	86.9758	1727	2790	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	86.8451	1775	2790	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	86.4644	1709	2790	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.5734	1396	2790	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.4644	1315	2790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,321] [INFO] DFAST Taxonomy check result was written to GCF_008123965.1_ASM812396v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:58,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:58,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:58,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/checkm_data
[2024-01-24 13:32:58,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:58,407] [INFO] Task started: CheckM
[2024-01-24 13:32:58,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008123965.1_ASM812396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008123965.1_ASM812396v1_genomic.fna/checkm_input GCF_008123965.1_ASM812396v1_genomic.fna/checkm_result
[2024-01-24 13:34:11,426] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:11,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:11,454] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:11,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:11,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008123965.1_ASM812396v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:11,455] [INFO] Task started: Blastn
[2024-01-24 13:34:11,455] [INFO] Running command: blastn -query GCF_008123965.1_ASM812396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb1723d9-085d-4bc2-bee9-5dd25c612fab/dqc_reference/reference_markers_gtdb.fasta -out GCF_008123965.1_ASM812396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:13,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:13,550] [INFO] Selected 21 target genomes.
[2024-01-24 13:34:13,550] [INFO] Target genome list was writen to GCF_008123965.1_ASM812396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:13,567] [INFO] Task started: fastANI
[2024-01-24 13:34:13,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0365097-223a-451f-a5d9-65c623b52959/GCF_008123965.1_ASM812396v1_genomic.fna.gz --refList GCF_008123965.1_ASM812396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008123965.1_ASM812396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:56,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:56,161] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:56,162] [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_008123965.1	s__Bradyrhizobium hipponense	100.0	2775	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	88.1431	1897	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	88.1349	1740	2790	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	88.061	1937	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_000938255.1	s__Bradyrhizobium sp000938255	87.8871	1747	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	87.8495	1783	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	87.7991	1749	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284375.1	s__Bradyrhizobium japonicum	87.7156	1842	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_008932115.1	s__Bradyrhizobium betae	87.6637	1639	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624505.1	s__Bradyrhizobium sp015624505	87.4649	1679	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	87.3849	1792	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_004212635.1	s__Bradyrhizobium sp004212635	87.3538	1837	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.55	95.55	0.86	0.86	2	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	87.3348	1762	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_004114935.1	s__Bradyrhizobium zhanjiangense	87.2547	1967	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.50	97.97	0.92	0.89	4	-
GCF_001641635.1	s__Bradyrhizobium centrolobii	87.2106	1832	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131015.1	s__Bradyrhizobium diazoefficiens_B	87.1077	1595	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	87.1068	1699	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	87.1029	1649	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641695.1	s__Bradyrhizobium neotropicale	87.0684	1761	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.88	0.88	2	-
GCF_000473045.1	s__Bradyrhizobium sp000473045	86.9273	1806	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	86.8793	1724	2790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:56,163] [INFO] GTDB search result was written to GCF_008123965.1_ASM812396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:56,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:56,168] [INFO] DFAST_QC result json was written to GCF_008123965.1_ASM812396v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:56,169] [INFO] DFAST_QC completed!
[2024-01-24 13:34:56,169] [INFO] Total running time: 0h3m12s