[2024-01-24 13:46:18,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference
[2024-01-24 13:46:19,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,973] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,974] [INFO] Running command: gunzip -c /var/lib/cwl/stga6dfb35d-0e90-4caf-befe-b0501c32c9fc/GCF_011516645.4_ASM1151664v4_genomic.fna.gz | prodigal -d GCF_011516645.4_ASM1151664v4_genomic.fna/cds.fna -a GCF_011516645.4_ASM1151664v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:53,336] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:53,337] [INFO] Task started: HMMsearch
[2024-01-24 13:46:53,337] [INFO] Running command: hmmsearch --tblout GCF_011516645.4_ASM1151664v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/reference_markers.hmm GCF_011516645.4_ASM1151664v4_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:53,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:53,850] [INFO] Found 6/6 markers.
[2024-01-24 13:46:53,929] [INFO] Query marker FASTA was written to GCF_011516645.4_ASM1151664v4_genomic.fna/markers.fasta
[2024-01-24 13:46:53,930] [INFO] Task started: Blastn
[2024-01-24 13:46:53,930] [INFO] Running command: blastn -query GCF_011516645.4_ASM1151664v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/reference_markers.fasta -out GCF_011516645.4_ASM1151664v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:55,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:55,096] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:55,097] [INFO] Target genome list was writen to GCF_011516645.4_ASM1151664v4_genomic.fna/target_genomes.txt
[2024-01-24 13:46:55,127] [INFO] Task started: fastANI
[2024-01-24 13:46:55,127] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dfb35d-0e90-4caf-befe-b0501c32c9fc/GCF_011516645.4_ASM1151664v4_genomic.fna.gz --refList GCF_011516645.4_ASM1151664v4_genomic.fna/target_genomes.txt --output GCF_011516645.4_ASM1151664v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:40,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:40,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:40,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:40,925] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:40,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:40,925] [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 septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	100.0	3457	3468	95	conclusive
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	91.1409	2323	3468	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	90.49	2139	3468	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	90.3946	2038	3468	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	90.391	2202	3468	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.3153	2322	3468	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.2831	2319	3468	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	90.2413	2204	3468	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	89.9885	2029	3468	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	89.9383	2004	3468	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	89.9372	2147	3468	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	89.8515	2112	3468	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	89.7568	2063	3468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:40,927] [INFO] DFAST Taxonomy check result was written to GCF_011516645.4_ASM1151664v4_genomic.fna/tc_result.tsv
[2024-01-24 13:47:40,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:40,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:40,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/checkm_data
[2024-01-24 13:47:40,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:41,039] [INFO] Task started: CheckM
[2024-01-24 13:47:41,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011516645.4_ASM1151664v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011516645.4_ASM1151664v4_genomic.fna/checkm_input GCF_011516645.4_ASM1151664v4_genomic.fna/checkm_result
[2024-01-24 13:49:18,280] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:18,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:18,307] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:18,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:18,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011516645.4_ASM1151664v4_genomic.fna/markers.fasta)
[2024-01-24 13:49:18,309] [INFO] Task started: Blastn
[2024-01-24 13:49:18,309] [INFO] Running command: blastn -query GCF_011516645.4_ASM1151664v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7303b4-44ca-4210-8c43-1bcfcff55ec2/dqc_reference/reference_markers_gtdb.fasta -out GCF_011516645.4_ASM1151664v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:20,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:20,651] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:20,651] [INFO] Target genome list was writen to GCF_011516645.4_ASM1151664v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:20,662] [INFO] Task started: fastANI
[2024-01-24 13:49:20,662] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dfb35d-0e90-4caf-befe-b0501c32c9fc/GCF_011516645.4_ASM1151664v4_genomic.fna.gz --refList GCF_011516645.4_ASM1151664v4_genomic.fna/target_genomes_gtdb.txt --output GCF_011516645.4_ASM1151664v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:08,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,675] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:08,675] [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_011516645.2	s__Bradyrhizobium septentrionale	99.9945	3452	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	conclusive
GCF_013373795.1	s__Bradyrhizobium quebecense	91.18	2304	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	90.8745	2151	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_003001755.1	s__Bradyrhizobium sp003001755	90.688	2063	3468	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	90.4934	2140	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	90.3557	2232	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379145.1	s__Bradyrhizobium elkanii	90.2927	2327	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_018130545.1	s__Bradyrhizobium tropiciagri_A	90.2639	2119	3468	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	90.2367	2205	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	90.0992	2162	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	90.0563	2041	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	89.9416	2147	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189235.2	s__Bradyrhizobium embrapense	89.8457	2111	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	89.7993	2191	3468	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,676] [INFO] GTDB search result was written to GCF_011516645.4_ASM1151664v4_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:08,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:08,680] [INFO] DFAST_QC result json was written to GCF_011516645.4_ASM1151664v4_genomic.fna/dqc_result.json
[2024-01-24 13:50:08,680] [INFO] DFAST_QC completed!
[2024-01-24 13:50:08,681] [INFO] Total running time: 0h3m50s