[2024-01-24 14:47:08,573] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference
[2024-01-24 14:47:10,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:10,075] [INFO] Task started: Prodigal
[2024-01-24 14:47:10,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c461410-8cc8-4b12-b04f-8eae4ce8934e/GCF_000472965.1_ASM47296v1_genomic.fna.gz | prodigal -d GCF_000472965.1_ASM47296v1_genomic.fna/cds.fna -a GCF_000472965.1_ASM47296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:35,283] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:35,283] [INFO] Task started: HMMsearch
[2024-01-24 14:47:35,283] [INFO] Running command: hmmsearch --tblout GCF_000472965.1_ASM47296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/reference_markers.hmm GCF_000472965.1_ASM47296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:35,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:35,705] [INFO] Found 6/6 markers.
[2024-01-24 14:47:35,771] [INFO] Query marker FASTA was written to GCF_000472965.1_ASM47296v1_genomic.fna/markers.fasta
[2024-01-24 14:47:35,771] [INFO] Task started: Blastn
[2024-01-24 14:47:35,771] [INFO] Running command: blastn -query GCF_000472965.1_ASM47296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/reference_markers.fasta -out GCF_000472965.1_ASM47296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:36,798] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:36,802] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:36,802] [INFO] Target genome list was writen to GCF_000472965.1_ASM47296v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:36,807] [INFO] Task started: fastANI
[2024-01-24 14:47:36,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c461410-8cc8-4b12-b04f-8eae4ce8934e/GCF_000472965.1_ASM47296v1_genomic.fna.gz --refList GCF_000472965.1_ASM47296v1_genomic.fna/target_genomes.txt --output GCF_000472965.1_ASM47296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:07,950] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:07,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:07,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:07,964] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:07,964] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:07,965] [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 murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	100.0	2607	2613	95	conclusive
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	93.5462	2039	2613	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	91.3787	2062	2613	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	90.4517	1931	2613	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	88.5	1922	2613	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	88.2436	1956	2613	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	88.0928	1922	2613	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	87.498	1840	2613	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	83.1076	1225	2613	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.6856	1456	2613	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.5176	1332	2613	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.5052	1337	2613	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.4905	1411	2613	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:07,966] [INFO] DFAST Taxonomy check result was written to GCF_000472965.1_ASM47296v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:07,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:07,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:07,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/checkm_data
[2024-01-24 14:48:07,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:08,041] [INFO] Task started: CheckM
[2024-01-24 14:48:08,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000472965.1_ASM47296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000472965.1_ASM47296v1_genomic.fna/checkm_input GCF_000472965.1_ASM47296v1_genomic.fna/checkm_result
[2024-01-24 14:49:16,738] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:16,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:16,764] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:16,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:16,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000472965.1_ASM47296v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:16,765] [INFO] Task started: Blastn
[2024-01-24 14:49:16,765] [INFO] Running command: blastn -query GCF_000472965.1_ASM47296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6325f978-c0ab-42ae-90fa-7d3a3e79215f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000472965.1_ASM47296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:18,823] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:18,826] [INFO] Selected 12 target genomes.
[2024-01-24 14:49:18,826] [INFO] Target genome list was writen to GCF_000472965.1_ASM47296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:18,837] [INFO] Task started: fastANI
[2024-01-24 14:49:18,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c461410-8cc8-4b12-b04f-8eae4ce8934e/GCF_000472965.1_ASM47296v1_genomic.fna.gz --refList GCF_000472965.1_ASM47296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000472965.1_ASM47296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:47,890] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:47,902] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:47,902] [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_000472965.1	s__Bradyrhizobium murdochi	100.0	2607	2613	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_018398875.1	s__Bradyrhizobium sp018398875	94.5167	2102	2613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693485.1	s__Bradyrhizobium sp001693485	93.7708	2131	2613	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	93.5422	2039	2613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398895.1	s__Bradyrhizobium sp018398895	91.7508	2021	2613	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	91.3553	2065	2613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114825.1	s__Bradyrhizobium australiense	90.4557	1931	2613	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	88.2633	1939	2613	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	88.2581	1953	2613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596315.1	s__Bradyrhizobium sp018596315	88.1408	1914	2613	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	88.0908	1922	2613	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305715.1	s__Bradyrhizobium sp017305715	83.902	1435	2613	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 14:49:47,904] [INFO] GTDB search result was written to GCF_000472965.1_ASM47296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:47,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:47,911] [INFO] DFAST_QC result json was written to GCF_000472965.1_ASM47296v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:47,912] [INFO] DFAST_QC completed!
[2024-01-24 14:49:47,912] [INFO] Total running time: 0h2m39s