[2024-01-24 13:21:46,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference
[2024-01-24 13:21:47,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,710] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgab00c786-75cb-4e74-b73b-3d26be8cdc86/GCF_013178945.1_ASM1317894v1_genomic.fna.gz | prodigal -d GCF_013178945.1_ASM1317894v1_genomic.fna/cds.fna -a GCF_013178945.1_ASM1317894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:11,763] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:11,763] [INFO] Task started: HMMsearch
[2024-01-24 13:22:11,764] [INFO] Running command: hmmsearch --tblout GCF_013178945.1_ASM1317894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/reference_markers.hmm GCF_013178945.1_ASM1317894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:12,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:12,175] [INFO] Found 6/6 markers.
[2024-01-24 13:22:12,236] [INFO] Query marker FASTA was written to GCF_013178945.1_ASM1317894v1_genomic.fna/markers.fasta
[2024-01-24 13:22:12,236] [INFO] Task started: Blastn
[2024-01-24 13:22:12,236] [INFO] Running command: blastn -query GCF_013178945.1_ASM1317894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/reference_markers.fasta -out GCF_013178945.1_ASM1317894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:13,411] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:13,415] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:13,415] [INFO] Target genome list was writen to GCF_013178945.1_ASM1317894v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:13,421] [INFO] Task started: fastANI
[2024-01-24 13:22:13,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgab00c786-75cb-4e74-b73b-3d26be8cdc86/GCF_013178945.1_ASM1317894v1_genomic.fna.gz --refList GCF_013178945.1_ASM1317894v1_genomic.fna/target_genomes.txt --output GCF_013178945.1_ASM1317894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:51,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:51,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:51,284] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:51,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:51,285] [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 aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	100.0	2489	2490	95	conclusive
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	88.6062	2097	2490	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	82.3076	1383	2490	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	82.2779	1397	2490	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	82.2318	1369	2490	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	82.1818	1269	2490	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	82.0785	1348	2490	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	82.0589	1413	2490	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.0423	1279	2490	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.0379	1297	2490	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	82.0358	1276	2490	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	81.9968	1329	2490	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	81.9609	1257	2490	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	81.9394	1263	2490	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	81.8933	1198	2490	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	81.8786	1189	2490	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	81.809	1362	2490	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	81.7956	1327	2490	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	81.6589	1259	2490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,287] [INFO] DFAST Taxonomy check result was written to GCF_013178945.1_ASM1317894v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:51,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:51,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:51,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/checkm_data
[2024-01-24 13:22:51,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:51,363] [INFO] Task started: CheckM
[2024-01-24 13:22:51,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013178945.1_ASM1317894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013178945.1_ASM1317894v1_genomic.fna/checkm_input GCF_013178945.1_ASM1317894v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,464] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,493] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013178945.1_ASM1317894v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,495] [INFO] Task started: Blastn
[2024-01-24 13:24:00,495] [INFO] Running command: blastn -query GCF_013178945.1_ASM1317894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3baf3134-02ba-4b7e-91e2-61da79968c69/dqc_reference/reference_markers_gtdb.fasta -out GCF_013178945.1_ASM1317894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:02,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:02,824] [INFO] Selected 9 target genomes.
[2024-01-24 13:24:02,825] [INFO] Target genome list was writen to GCF_013178945.1_ASM1317894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:02,923] [INFO] Task started: fastANI
[2024-01-24 13:24:02,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgab00c786-75cb-4e74-b73b-3d26be8cdc86/GCF_013178945.1_ASM1317894v1_genomic.fna.gz --refList GCF_013178945.1_ASM1317894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013178945.1_ASM1317894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:25,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:25,193] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:25,194] [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_013178945.1	s__Bradyrhizobium sp013178945	100.0	2489	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.74	98.70	0.95	0.95	3	conclusive
GCF_900176205.1	s__Bradyrhizobium sp900176205	89.1323	2094	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000239775.1	s__Bradyrhizobium sp000239775	89.1032	1871	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239795.1	s__Bradyrhizobium sp000239795	88.8323	1688	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344805.1	s__Bradyrhizobium oligotrophicum	88.6077	2097	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026145.1	s__Bradyrhizobium sp000026145	88.5186	1971	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015165.1	s__Bradyrhizobium denitrificans	87.5244	1948	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.10	98.93	0.93	0.90	4	-
GCF_001982635.1	s__Bradyrhizobium mercantei	82.166	1271	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831585.1	s__Bradyrhizobium sp002831585	81.8786	1316	2490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.70	98.62	0.95	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:25,195] [INFO] GTDB search result was written to GCF_013178945.1_ASM1317894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:25,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:25,199] [INFO] DFAST_QC result json was written to GCF_013178945.1_ASM1317894v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:25,199] [INFO] DFAST_QC completed!
[2024-01-24 13:24:25,200] [INFO] Total running time: 0h2m39s