[2024-01-25 20:13:50,830] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference
[2024-01-25 20:13:51,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,989] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg11e6239b-5ef9-446f-9dac-b5d47aa6dbca/GCF_009720755.1_ASM972075v1_genomic.fna.gz | prodigal -d GCF_009720755.1_ASM972075v1_genomic.fna/cds.fna -a GCF_009720755.1_ASM972075v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:05,939] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:05,940] [INFO] Task started: HMMsearch
[2024-01-25 20:14:05,940] [INFO] Running command: hmmsearch --tblout GCF_009720755.1_ASM972075v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/reference_markers.hmm GCF_009720755.1_ASM972075v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:06,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:06,249] [INFO] Found 6/6 markers.
[2024-01-25 20:14:06,306] [INFO] Query marker FASTA was written to GCF_009720755.1_ASM972075v1_genomic.fna/markers.fasta
[2024-01-25 20:14:06,306] [INFO] Task started: Blastn
[2024-01-25 20:14:06,306] [INFO] Running command: blastn -query GCF_009720755.1_ASM972075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/reference_markers.fasta -out GCF_009720755.1_ASM972075v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:07,376] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:07,379] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:07,379] [INFO] Target genome list was writen to GCF_009720755.1_ASM972075v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:07,389] [INFO] Task started: fastANI
[2024-01-25 20:14:07,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e6239b-5ef9-446f-9dac-b5d47aa6dbca/GCF_009720755.1_ASM972075v1_genomic.fna.gz --refList GCF_009720755.1_ASM972075v1_genomic.fna/target_genomes.txt --output GCF_009720755.1_ASM972075v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:27,935] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:27,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:27,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:27,945] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:27,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:27,945] [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
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	97.8969	1339	1808	95	conclusive
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	85.4178	1272	1808	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	85.2678	1096	1808	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	84.6945	1175	1808	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	78.1686	625	1808	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	78.0451	592	1808	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	78.0197	611	1808	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	78.0002	609	1808	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.8716	558	1808	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.8271	509	1808	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.5783	685	1808	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.4487	541	1808	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.3922	682	1808	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.1672	635	1808	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.1338	367	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:27,946] [INFO] DFAST Taxonomy check result was written to GCF_009720755.1_ASM972075v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:27,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:27,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:27,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/checkm_data
[2024-01-25 20:14:27,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:28,001] [INFO] Task started: CheckM
[2024-01-25 20:14:28,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720755.1_ASM972075v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720755.1_ASM972075v1_genomic.fna/checkm_input GCF_009720755.1_ASM972075v1_genomic.fna/checkm_result
[2024-01-25 20:15:28,079] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:28,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:28,099] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:28,099] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:28,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720755.1_ASM972075v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:28,102] [INFO] Task started: Blastn
[2024-01-25 20:15:28,102] [INFO] Running command: blastn -query GCF_009720755.1_ASM972075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4069a64e-cfa3-40f7-9233-2f2dd56d7315/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720755.1_ASM972075v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:30,313] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:30,317] [INFO] Selected 6 target genomes.
[2024-01-25 20:15:30,317] [INFO] Target genome list was writen to GCF_009720755.1_ASM972075v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:30,321] [INFO] Task started: fastANI
[2024-01-25 20:15:30,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg11e6239b-5ef9-446f-9dac-b5d47aa6dbca/GCF_009720755.1_ASM972075v1_genomic.fna.gz --refList GCF_009720755.1_ASM972075v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720755.1_ASM972075v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:40,680] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:40,685] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:40,685] [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
GCA_009720755.1	s__Rhodoplanes serenus	100.0	1804	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	conclusive
GCF_016653355.1	s__Rhodoplanes elegans	85.4257	1271	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCA_013377085.1	s__Rhodoplanes sp013377085	84.9729	1303	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	84.6966	1173	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293785.1	s__Rhodoplanes sp000293785	82.6142	1016	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	79.0986	582	1808	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:40,687] [INFO] GTDB search result was written to GCF_009720755.1_ASM972075v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:40,688] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:40,691] [INFO] DFAST_QC result json was written to GCF_009720755.1_ASM972075v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:40,691] [INFO] DFAST_QC completed!
[2024-01-25 20:15:40,691] [INFO] Total running time: 0h1m50s