[2024-01-24 13:01:12,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference
[2024-01-24 13:01:14,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:14,118] [INFO] Task started: Prodigal
[2024-01-24 13:01:14,118] [INFO] Running command: gunzip -c /var/lib/cwl/stga4d41fad-14b0-41ab-a834-56cf56be0f5b/GCF_001542415.1_ASM154241v1_genomic.fna.gz | prodigal -d GCF_001542415.1_ASM154241v1_genomic.fna/cds.fna -a GCF_001542415.1_ASM154241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:39,548] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:39,549] [INFO] Task started: HMMsearch
[2024-01-24 13:01:39,549] [INFO] Running command: hmmsearch --tblout GCF_001542415.1_ASM154241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/reference_markers.hmm GCF_001542415.1_ASM154241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:39,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:39,960] [INFO] Found 6/6 markers.
[2024-01-24 13:01:40,029] [INFO] Query marker FASTA was written to GCF_001542415.1_ASM154241v1_genomic.fna/markers.fasta
[2024-01-24 13:01:40,029] [INFO] Task started: Blastn
[2024-01-24 13:01:40,030] [INFO] Running command: blastn -query GCF_001542415.1_ASM154241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/reference_markers.fasta -out GCF_001542415.1_ASM154241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:41,104] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:41,110] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:41,111] [INFO] Target genome list was writen to GCF_001542415.1_ASM154241v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:41,117] [INFO] Task started: fastANI
[2024-01-24 13:01:41,117] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d41fad-14b0-41ab-a834-56cf56be0f5b/GCF_001542415.1_ASM154241v1_genomic.fna.gz --refList GCF_001542415.1_ASM154241v1_genomic.fna/target_genomes.txt --output GCF_001542415.1_ASM154241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:18,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:18,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:18,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:18,947] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:18,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:18,947] [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 macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	100.0	2834	2839	95	conclusive
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	87.8818	1979	2839	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	87.3153	1878	2839	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	87.2389	1935	2839	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	87.2278	1945	2839	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	87.1876	1908	2839	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	87.1617	1931	2839	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	87.1044	1913	2839	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	87.0985	1920	2839	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	87.0935	1783	2839	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	87.0621	1900	2839	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	87.0011	1779	2839	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	86.9462	1927	2839	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	86.8957	1772	2839	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	86.8422	1818	2839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:18,949] [INFO] DFAST Taxonomy check result was written to GCF_001542415.1_ASM154241v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:18,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:18,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:18,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/checkm_data
[2024-01-24 13:02:18,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:19,029] [INFO] Task started: CheckM
[2024-01-24 13:02:19,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001542415.1_ASM154241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001542415.1_ASM154241v1_genomic.fna/checkm_input GCF_001542415.1_ASM154241v1_genomic.fna/checkm_result
[2024-01-24 13:03:27,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:27,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:27,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:27,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:27,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001542415.1_ASM154241v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:27,750] [INFO] Task started: Blastn
[2024-01-24 13:03:27,750] [INFO] Running command: blastn -query GCF_001542415.1_ASM154241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa2e0d7b-cac9-4795-92ae-0a198dd76eed/dqc_reference/reference_markers_gtdb.fasta -out GCF_001542415.1_ASM154241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:29,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:29,734] [INFO] Selected 18 target genomes.
[2024-01-24 13:03:29,734] [INFO] Target genome list was writen to GCF_001542415.1_ASM154241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:29,778] [INFO] Task started: fastANI
[2024-01-24 13:03:29,779] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d41fad-14b0-41ab-a834-56cf56be0f5b/GCF_001542415.1_ASM154241v1_genomic.fna.gz --refList GCF_001542415.1_ASM154241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001542415.1_ASM154241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:09,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:09,649] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:09,649] [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_001542415.1	s__Bradyrhizobium macuxiense	100.0	2835	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001982635.1	s__Bradyrhizobium mercantei	87.914	1974	2839	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	87.6131	2004	2839	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	87.4835	1845	2839	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	87.4394	1877	2839	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	87.3761	1861	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_000379145.1	s__Bradyrhizobium elkanii	87.256	1934	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_013373795.1	s__Bradyrhizobium quebecense	87.1812	1897	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	87.1553	1932	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	87.1508	1984	2839	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	87.1283	1789	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	87.0731	1925	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	87.0466	1904	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_000938305.1	s__Bradyrhizobium sp000938305	87.0075	1761	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.61	95.61	0.87	0.87	2	-
GCF_900696085.1	s__Bradyrhizobium ivorense	86.9252	1931	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.20	96.86	0.90	0.88	3	-
GCF_018130215.1	s__Bradyrhizobium jicamae_A	86.7867	1789	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.26	99.26	0.93	0.93	2	-
GCF_018130695.1	s__Bradyrhizobium jicamae_B	85.3484	1677	2839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131005.1	s__Bradyrhizobium lablabi_D	84.9097	1529	2839	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 13:04:09,653] [INFO] GTDB search result was written to GCF_001542415.1_ASM154241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:09,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:09,657] [INFO] DFAST_QC result json was written to GCF_001542415.1_ASM154241v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:09,657] [INFO] DFAST_QC completed!
[2024-01-24 13:04:09,657] [INFO] Total running time: 0h2m57s