[2024-01-24 14:38:47,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,419] [INFO] DQC Reference Directory: /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference
[2024-01-24 14:38:48,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,726] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg2979842e-2f38-4564-8fbc-eedc9a019768/GCF_019402665.1_ASM1940266v1_genomic.fna.gz | prodigal -d GCF_019402665.1_ASM1940266v1_genomic.fna/cds.fna -a GCF_019402665.1_ASM1940266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:14,877] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:14,877] [INFO] Task started: HMMsearch
[2024-01-24 14:39:14,877] [INFO] Running command: hmmsearch --tblout GCF_019402665.1_ASM1940266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/reference_markers.hmm GCF_019402665.1_ASM1940266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:15,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:15,235] [INFO] Found 6/6 markers.
[2024-01-24 14:39:15,300] [INFO] Query marker FASTA was written to GCF_019402665.1_ASM1940266v1_genomic.fna/markers.fasta
[2024-01-24 14:39:15,301] [INFO] Task started: Blastn
[2024-01-24 14:39:15,301] [INFO] Running command: blastn -query GCF_019402665.1_ASM1940266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/reference_markers.fasta -out GCF_019402665.1_ASM1940266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:16,366] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:16,369] [INFO] Selected 22 target genomes.
[2024-01-24 14:39:16,370] [INFO] Target genome list was writen to GCF_019402665.1_ASM1940266v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:16,383] [INFO] Task started: fastANI
[2024-01-24 14:39:16,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg2979842e-2f38-4564-8fbc-eedc9a019768/GCF_019402665.1_ASM1940266v1_genomic.fna.gz --refList GCF_019402665.1_ASM1940266v1_genomic.fna/target_genomes.txt --output GCF_019402665.1_ASM1940266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:06,528] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:06,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:06,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:06,551] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:06,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:06,552] [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 canariense	strain=BTA-1	GCA_019402665.1	255045	255045	suspected-type	True	100.0	2776	2781	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	88.875	1970	2781	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	88.8134	1994	2781	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.7488	1978	2781	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	88.6275	1940	2781	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	88.5937	1930	2781	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	88.5838	1967	2781	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.5736	1742	2781	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	88.4123	1940	2781	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	88.3941	1812	2781	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	88.3095	1797	2781	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.2563	1805	2781	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.2353	1865	2781	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.2336	1930	2781	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	88.2158	2009	2781	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	87.994	1951	2781	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	87.9394	1859	2781	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	87.8964	1872	2781	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	87.6111	1856	2781	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	87.6061	1926	2781	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.6117	1439	2781	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.4356	1364	2781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:06,553] [INFO] DFAST Taxonomy check result was written to GCF_019402665.1_ASM1940266v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:06,554] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:06,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:06,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/checkm_data
[2024-01-24 14:40:06,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:06,639] [INFO] Task started: CheckM
[2024-01-24 14:40:06,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019402665.1_ASM1940266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019402665.1_ASM1940266v1_genomic.fna/checkm_input GCF_019402665.1_ASM1940266v1_genomic.fna/checkm_result
[2024-01-24 14:41:17,704] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:17,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:17,735] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:17,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:17,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019402665.1_ASM1940266v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:17,737] [INFO] Task started: Blastn
[2024-01-24 14:41:17,737] [INFO] Running command: blastn -query GCF_019402665.1_ASM1940266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb095669e-8c83-43e6-9d7a-541e10bca242/dqc_reference/reference_markers_gtdb.fasta -out GCF_019402665.1_ASM1940266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:20,214] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:20,219] [INFO] Selected 6 target genomes.
[2024-01-24 14:41:20,219] [INFO] Target genome list was writen to GCF_019402665.1_ASM1940266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:20,227] [INFO] Task started: fastANI
[2024-01-24 14:41:20,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg2979842e-2f38-4564-8fbc-eedc9a019768/GCF_019402665.1_ASM1940266v1_genomic.fna.gz --refList GCF_019402665.1_ASM1940266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019402665.1_ASM1940266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:36,631] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:36,638] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:36,638] [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_000244935.1	s__Bradyrhizobium sp000244935	98.1324	2436	2781	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_000244915.1	s__Bradyrhizobium sp000244915	94.3704	2055	2781	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.18	98.18	0.85	0.85	2	-
GCF_016907215.1	s__Bradyrhizobium canariense	94.2261	2139	2781	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.32	98.14	0.85	0.84	16	-
GCF_000515415.1	s__Bradyrhizobium sp000515415	94.0218	2083	2781	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.36	95.36	0.85	0.85	2	-
GCF_003020115.1	s__Bradyrhizobium sp003020115	93.9309	1995	2781	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130465.1	s__Bradyrhizobium canariense_C	93.1362	1965	2781	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 14:41:36,640] [INFO] GTDB search result was written to GCF_019402665.1_ASM1940266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:36,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:36,647] [INFO] DFAST_QC result json was written to GCF_019402665.1_ASM1940266v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:36,647] [INFO] DFAST_QC completed!
[2024-01-24 14:41:36,647] [INFO] Total running time: 0h2m49s