[2024-01-25 18:03:20,450] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:20,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:20,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference
[2024-01-25 18:03:21,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:21,605] [INFO] Task started: Prodigal
[2024-01-25 18:03:21,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg543d3dfb-ed0f-45b6-ae8a-77457956d8e4/GCF_020329435.1_ASM2032943v1_genomic.fna.gz | prodigal -d GCF_020329435.1_ASM2032943v1_genomic.fna/cds.fna -a GCF_020329435.1_ASM2032943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:42,763] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:42,764] [INFO] Task started: HMMsearch
[2024-01-25 18:03:42,764] [INFO] Running command: hmmsearch --tblout GCF_020329435.1_ASM2032943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/reference_markers.hmm GCF_020329435.1_ASM2032943v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:43,077] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:43,078] [INFO] Found 6/6 markers.
[2024-01-25 18:03:43,135] [INFO] Query marker FASTA was written to GCF_020329435.1_ASM2032943v1_genomic.fna/markers.fasta
[2024-01-25 18:03:43,136] [INFO] Task started: Blastn
[2024-01-25 18:03:43,136] [INFO] Running command: blastn -query GCF_020329435.1_ASM2032943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/reference_markers.fasta -out GCF_020329435.1_ASM2032943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:44,022] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:44,025] [INFO] Selected 19 target genomes.
[2024-01-25 18:03:44,025] [INFO] Target genome list was writen to GCF_020329435.1_ASM2032943v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:44,032] [INFO] Task started: fastANI
[2024-01-25 18:03:44,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg543d3dfb-ed0f-45b6-ae8a-77457956d8e4/GCF_020329435.1_ASM2032943v1_genomic.fna.gz --refList GCF_020329435.1_ASM2032943v1_genomic.fna/target_genomes.txt --output GCF_020329435.1_ASM2032943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:22,818] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:22,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:22,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:22,832] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:04:22,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:04:22,832] [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 archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	88.1532	1894	2592	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	87.8485	2006	2592	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	87.7786	1935	2592	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	87.6355	1921	2592	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	87.4915	1898	2592	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	87.4769	1962	2592	95	below_threshold
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	87.1576	1966	2592	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	86.884	1842	2592	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	82.7099	1486	2592	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	82.6685	1210	2592	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	82.5964	1366	2592	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	82.5079	1408	2592	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	82.4885	1422	2592	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.4346	1391	2592	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.4327	1302	2592	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	82.4325	1476	2592	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	82.4173	1308	2592	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.4087	1327	2592	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	82.3287	1346	2592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:22,835] [INFO] DFAST Taxonomy check result was written to GCF_020329435.1_ASM2032943v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:22,836] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:22,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:22,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/checkm_data
[2024-01-25 18:04:22,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:22,911] [INFO] Task started: CheckM
[2024-01-25 18:04:22,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020329435.1_ASM2032943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020329435.1_ASM2032943v1_genomic.fna/checkm_input GCF_020329435.1_ASM2032943v1_genomic.fna/checkm_result
[2024-01-25 18:05:21,127] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:21,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:21,146] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:21,146] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:21,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020329435.1_ASM2032943v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:21,147] [INFO] Task started: Blastn
[2024-01-25 18:05:21,147] [INFO] Running command: blastn -query GCF_020329435.1_ASM2032943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb892ea4-6337-473e-a546-7c158ce1966b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020329435.1_ASM2032943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:23,125] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:23,128] [INFO] Selected 20 target genomes.
[2024-01-25 18:05:23,129] [INFO] Target genome list was writen to GCF_020329435.1_ASM2032943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:23,152] [INFO] Task started: fastANI
[2024-01-25 18:05:23,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg543d3dfb-ed0f-45b6-ae8a-77457956d8e4/GCF_020329435.1_ASM2032943v1_genomic.fna.gz --refList GCF_020329435.1_ASM2032943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020329435.1_ASM2032943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:07,231] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:07,244] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:06:07,244] [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_013114835.1	s__Bradyrhizobium archetypum	88.1549	1892	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472965.1	s__Bradyrhizobium murdochi	87.8591	2004	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440405.1	s__Bradyrhizobium valentinum	87.7807	1934	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	99.35	0.91	0.91	2	-
GCF_001693485.1	s__Bradyrhizobium sp001693485	87.7679	1972	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693515.2	s__Bradyrhizobium paxllaeri	87.6309	1922	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009930815.1	s__Bradyrhizobium sp009930815	87.4934	2021	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440475.1	s__Bradyrhizobium lablabi	87.4853	1900	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693385.1	s__Bradyrhizobium icense	87.4839	1962	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003062295.1	s__Bradyrhizobium algeriense	87.2342	1916	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440415.1	s__Bradyrhizobium retamae	87.1673	1965	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398875.1	s__Bradyrhizobium sp018398875	87.1543	2027	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130385.1	s__Bradyrhizobium sp018130385	87.0914	1703	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440395.1	s__Bradyrhizobium jicamae	86.8784	1842	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900696085.1	s__Bradyrhizobium ivorense	82.7178	1483	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.20	96.86	0.90	0.88	3	-
GCF_015624485.1	s__Bradyrhizobium sp015624485	82.5842	1346	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982635.1	s__Bradyrhizobium mercantei	82.5795	1369	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	82.5299	1420	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	82.496	1422	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	82.4446	1387	2592	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_018131005.1	s__Bradyrhizobium lablabi_D	81.7721	1222	2592	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 18:06:07,246] [INFO] GTDB search result was written to GCF_020329435.1_ASM2032943v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:07,246] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:07,249] [INFO] DFAST_QC result json was written to GCF_020329435.1_ASM2032943v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:07,250] [INFO] DFAST_QC completed!
[2024-01-25 18:06:07,250] [INFO] Total running time: 0h2m47s