[2024-01-24 12:21:53,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:53,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:53,914] [INFO] DQC Reference Directory: /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference
[2024-01-24 12:21:55,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:55,127] [INFO] Task started: Prodigal
[2024-01-24 12:21:55,127] [INFO] Running command: gunzip -c /var/lib/cwl/stgbece4ac5-0bc3-45d7-ba3d-8d5db898b6c6/GCF_006539665.1_ASM653966v1_genomic.fna.gz | prodigal -d GCF_006539665.1_ASM653966v1_genomic.fna/cds.fna -a GCF_006539665.1_ASM653966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:22,448] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:22,448] [INFO] Task started: HMMsearch
[2024-01-24 12:22:22,448] [INFO] Running command: hmmsearch --tblout GCF_006539665.1_ASM653966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/reference_markers.hmm GCF_006539665.1_ASM653966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:22,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:22,923] [INFO] Found 6/6 markers.
[2024-01-24 12:22:23,020] [INFO] Query marker FASTA was written to GCF_006539665.1_ASM653966v1_genomic.fna/markers.fasta
[2024-01-24 12:22:23,021] [INFO] Task started: Blastn
[2024-01-24 12:22:23,021] [INFO] Running command: blastn -query GCF_006539665.1_ASM653966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/reference_markers.fasta -out GCF_006539665.1_ASM653966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:24,124] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:24,127] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:24,128] [INFO] Target genome list was writen to GCF_006539665.1_ASM653966v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:24,132] [INFO] Task started: fastANI
[2024-01-24 12:22:24,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgbece4ac5-0bc3-45d7-ba3d-8d5db898b6c6/GCF_006539665.1_ASM653966v1_genomic.fna.gz --refList GCF_006539665.1_ASM653966v1_genomic.fna/target_genomes.txt --output GCF_006539665.1_ASM653966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:55,789] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:55,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:55,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:55,799] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:55,800] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:55,800] [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 elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	100.0	2933	2946	95	conclusive
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	99.999	2946	2946	95	conclusive
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	99.9977	2945	2946	95	conclusive
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	94.6425	2316	2946	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	90.7438	2163	2946	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	90.6441	1998	2946	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	90.6258	1985	2946	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	90.5042	2005	2946	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	90.4071	2154	2946	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	90.3287	2029	2946	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	90.2993	2069	2946	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	90.2604	2109	2946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,801] [INFO] DFAST Taxonomy check result was written to GCF_006539665.1_ASM653966v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:55,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:55,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:55,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/checkm_data
[2024-01-24 12:22:55,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:55,884] [INFO] Task started: CheckM
[2024-01-24 12:22:55,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539665.1_ASM653966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539665.1_ASM653966v1_genomic.fna/checkm_input GCF_006539665.1_ASM653966v1_genomic.fna/checkm_result
[2024-01-24 12:24:10,113] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:10,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,133] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:10,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:10,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539665.1_ASM653966v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:10,134] [INFO] Task started: Blastn
[2024-01-24 12:24:10,134] [INFO] Running command: blastn -query GCF_006539665.1_ASM653966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd537954c-7974-41f8-9020-8ed0cd5cabb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539665.1_ASM653966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:12,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:12,293] [INFO] Selected 17 target genomes.
[2024-01-24 12:24:12,293] [INFO] Target genome list was writen to GCF_006539665.1_ASM653966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:12,304] [INFO] Task started: fastANI
[2024-01-24 12:24:12,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgbece4ac5-0bc3-45d7-ba3d-8d5db898b6c6/GCF_006539665.1_ASM653966v1_genomic.fna.gz --refList GCF_006539665.1_ASM653966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539665.1_ASM653966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:51,752] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:51,766] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:51,766] [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_000379145.1	s__Bradyrhizobium elkanii	99.999	2946	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	conclusive
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	94.6425	2316	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_002532045.1	s__Bradyrhizobium sp002532045	91.4376	2191	2946	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	91.3909	2274	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001755.1	s__Bradyrhizobium sp003001755	91.3541	2035	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	91.1686	2058	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_001982635.1	s__Bradyrhizobium mercantei	91.1515	2055	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130545.1	s__Bradyrhizobium tropiciagri_A	90.864	2043	2946	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	90.7844	2088	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373795.1	s__Bradyrhizobium quebecense	90.7121	2149	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	90.7113	1989	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	90.4411	1945	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	90.4209	2152	2946	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	90.311	2068	2946	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	90.2785	2106	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	90.1667	2222	2946	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
GCF_018130505.1	s__Bradyrhizobium tropiciagri_B	88.4478	1815	2946	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 12:24:51,768] [INFO] GTDB search result was written to GCF_006539665.1_ASM653966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:51,768] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:51,772] [INFO] DFAST_QC result json was written to GCF_006539665.1_ASM653966v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:51,772] [INFO] DFAST_QC completed!
[2024-01-24 12:24:51,773] [INFO] Total running time: 0h2m58s