[2024-01-24 14:19:01,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference
[2024-01-24 14:19:02,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,671] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgb16779d4-5f36-44cc-b86b-7129811ec337/GCF_002068095.1_ASM206809v1_genomic.fna.gz | prodigal -d GCF_002068095.1_ASM206809v1_genomic.fna/cds.fna -a GCF_002068095.1_ASM206809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:29,537] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:29,538] [INFO] Task started: HMMsearch
[2024-01-24 14:19:29,538] [INFO] Running command: hmmsearch --tblout GCF_002068095.1_ASM206809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/reference_markers.hmm GCF_002068095.1_ASM206809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:29,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:29,926] [INFO] Found 6/6 markers.
[2024-01-24 14:19:30,000] [INFO] Query marker FASTA was written to GCF_002068095.1_ASM206809v1_genomic.fna/markers.fasta
[2024-01-24 14:19:30,000] [INFO] Task started: Blastn
[2024-01-24 14:19:30,000] [INFO] Running command: blastn -query GCF_002068095.1_ASM206809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/reference_markers.fasta -out GCF_002068095.1_ASM206809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:31,136] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:31,140] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:31,140] [INFO] Target genome list was writen to GCF_002068095.1_ASM206809v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:31,147] [INFO] Task started: fastANI
[2024-01-24 14:19:31,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16779d4-5f36-44cc-b86b-7129811ec337/GCF_002068095.1_ASM206809v1_genomic.fna.gz --refList GCF_002068095.1_ASM206809v1_genomic.fna/target_genomes.txt --output GCF_002068095.1_ASM206809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:17,478] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:17,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:17,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:17,498] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:17,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:17,498] [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 sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	100.0	2849	2863	95	conclusive
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	91.9779	2249	2863	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	90.4348	2098	2863	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.7754	2195	2863	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.7324	2206	2863	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.5928	2117	2863	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.1982	2166	2863	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.1632	2027	2863	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	89.0226	1952	2863	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.7083	1992	2863	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.696	1784	2863	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.6913	2021	2863	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	88.6862	1923	2863	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	88.637	1946	2863	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	88.6168	1935	2863	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	88.5438	1975	2863	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	88.5173	1900	2863	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.287	1975	2863	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.8096	1544	2863	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.793	1441	2863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,500] [INFO] DFAST Taxonomy check result was written to GCF_002068095.1_ASM206809v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:17,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:17,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:17,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/checkm_data
[2024-01-24 14:20:17,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:17,586] [INFO] Task started: CheckM
[2024-01-24 14:20:17,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002068095.1_ASM206809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002068095.1_ASM206809v1_genomic.fna/checkm_input GCF_002068095.1_ASM206809v1_genomic.fna/checkm_result
[2024-01-24 14:21:27,616] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:27,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:27,640] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:27,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:27,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002068095.1_ASM206809v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:27,641] [INFO] Task started: Blastn
[2024-01-24 14:21:27,642] [INFO] Running command: blastn -query GCF_002068095.1_ASM206809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ac2c462-7a41-4d3f-8695-983dbf32786f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002068095.1_ASM206809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:29,889] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:29,893] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:29,893] [INFO] Target genome list was writen to GCF_002068095.1_ASM206809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:29,927] [INFO] Task started: fastANI
[2024-01-24 14:21:29,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16779d4-5f36-44cc-b86b-7129811ec337/GCF_002068095.1_ASM206809v1_genomic.fna.gz --refList GCF_002068095.1_ASM206809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002068095.1_ASM206809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:56,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:56,119] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:56,119] [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_002068095.1	s__Bradyrhizobium sacchari	100.0	2847	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	conclusive
GCF_004216735.1	s__Bradyrhizobium sp004216735	93.8255	2204	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129405.1	s__Bradyrhizobium iriomotense_B	92.2883	2082	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	92.2727	2089	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	92.2141	2075	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830635.1	s__Bradyrhizobium huanghuaihaiense	91.9864	2248	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	91.5136	2182	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.7107	1889	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795245.1	s__Bradyrhizobium forestalis	89.1887	2023	2863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473065.1	s__Bradyrhizobium sp000473065	88.9971	1976	2863	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 14:21:56,121] [INFO] GTDB search result was written to GCF_002068095.1_ASM206809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:56,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:56,125] [INFO] DFAST_QC result json was written to GCF_002068095.1_ASM206809v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:56,125] [INFO] DFAST_QC completed!
[2024-01-24 14:21:56,125] [INFO] Total running time: 0h2m55s