[2024-01-24 10:47:23,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,182] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b2913b9-0933-4f9c-bb1a-d63e5d5233d7/GCF_030160735.1_ASM3016073v1_genomic.fna.gz | prodigal -d GCF_030160735.1_ASM3016073v1_genomic.fna/cds.fna -a GCF_030160735.1_ASM3016073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:46,885] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:46,886] [INFO] Task started: HMMsearch
[2024-01-24 10:47:46,886] [INFO] Running command: hmmsearch --tblout GCF_030160735.1_ASM3016073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/reference_markers.hmm GCF_030160735.1_ASM3016073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:47,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:47,230] [INFO] Found 6/6 markers.
[2024-01-24 10:47:47,292] [INFO] Query marker FASTA was written to GCF_030160735.1_ASM3016073v1_genomic.fna/markers.fasta
[2024-01-24 10:47:47,292] [INFO] Task started: Blastn
[2024-01-24 10:47:47,292] [INFO] Running command: blastn -query GCF_030160735.1_ASM3016073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/reference_markers.fasta -out GCF_030160735.1_ASM3016073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:48,412] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:48,417] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:48,418] [INFO] Target genome list was writen to GCF_030160735.1_ASM3016073v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:48,428] [INFO] Task started: fastANI
[2024-01-24 10:47:48,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2913b9-0933-4f9c-bb1a-d63e5d5233d7/GCF_030160735.1_ASM3016073v1_genomic.fna.gz --refList GCF_030160735.1_ASM3016073v1_genomic.fna/target_genomes.txt --output GCF_030160735.1_ASM3016073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:34,207] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:34,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:34,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:34,226] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:34,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:34,226] [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	95.1439	1888	2287	95	conclusive
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	90.9165	1781	2287	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	90.1841	1637	2287	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	90.0287	1690	2287	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	89.9346	1653	2287	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	89.9258	1769	2287	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	89.6129	1765	2287	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.6	1834	2287	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.3211	1797	2287	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.3165	1770	2287	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.3128	1820	2287	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	89.2225	1720	2287	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.1842	1745	2287	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.1418	1698	2287	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	89.1158	1810	2287	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.9934	1740	2287	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.8865	1732	2287	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	88.7727	1741	2287	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.3299	1619	2287	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.7269	1352	2287	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.7259	1268	2287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,228] [INFO] DFAST Taxonomy check result was written to GCF_030160735.1_ASM3016073v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:34,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:34,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:34,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/checkm_data
[2024-01-24 10:48:34,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:34,308] [INFO] Task started: CheckM
[2024-01-24 10:48:34,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160735.1_ASM3016073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160735.1_ASM3016073v1_genomic.fna/checkm_input GCF_030160735.1_ASM3016073v1_genomic.fna/checkm_result
[2024-01-24 10:49:35,219] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:35,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:35,243] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:35,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:35,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160735.1_ASM3016073v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:35,244] [INFO] Task started: Blastn
[2024-01-24 10:49:35,245] [INFO] Running command: blastn -query GCF_030160735.1_ASM3016073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86dd1bf8-b412-4da9-abdd-5aaa17fa7dc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160735.1_ASM3016073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:37,564] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:37,569] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:37,570] [INFO] Target genome list was writen to GCF_030160735.1_ASM3016073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:37,598] [INFO] Task started: fastANI
[2024-01-24 10:49:37,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2913b9-0933-4f9c-bb1a-d63e5d5233d7/GCF_030160735.1_ASM3016073v1_genomic.fna.gz --refList GCF_030160735.1_ASM3016073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160735.1_ASM3016073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:10,628] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:10,643] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:10,643] [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_015291725.1	s__Bradyrhizobium japonicum_D	95.5791	1960	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	conclusive
GCF_016031635.1	s__Bradyrhizobium diversitatis	95.1549	1887	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	93.2545	1854	2287	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	91.7695	1640	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556045.1	s__Bradyrhizobium sp001556045	91.467	1747	2287	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	91.4566	1761	2287	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	90.9111	1782	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473065.1	s__Bradyrhizobium sp000473065	90.7295	1723	2287	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	90.2233	1742	2287	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	89.9459	1764	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031625.1	s__Bradyrhizobium agreste	89.9345	1652	2287	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	89.9188	1770	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	95.91	0.89	0.81	9	-
GCF_004114935.1	s__Bradyrhizobium zhanjiangense	89.1966	1743	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.50	97.97	0.92	0.89	4	-
GCF_004571025.1	s__Bradyrhizobium niftali	88.9882	1740	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	88.8865	1732	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	87.3461	1601	2287	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 10:50:10,646] [INFO] GTDB search result was written to GCF_030160735.1_ASM3016073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:10,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:10,651] [INFO] DFAST_QC result json was written to GCF_030160735.1_ASM3016073v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:10,651] [INFO] DFAST_QC completed!
[2024-01-24 10:50:10,651] [INFO] Total running time: 0h2m47s