[2024-01-24 11:51:19,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference
[2024-01-24 11:51:20,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,748] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg40555c0b-38af-441e-91c4-f9bc1d31b65a/GCF_001642675.1_ASM164267v1_genomic.fna.gz | prodigal -d GCF_001642675.1_ASM164267v1_genomic.fna/cds.fna -a GCF_001642675.1_ASM164267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:49,048] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:49,049] [INFO] Task started: HMMsearch
[2024-01-24 11:51:49,049] [INFO] Running command: hmmsearch --tblout GCF_001642675.1_ASM164267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/reference_markers.hmm GCF_001642675.1_ASM164267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:49,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:49,408] [INFO] Found 6/6 markers.
[2024-01-24 11:51:49,474] [INFO] Query marker FASTA was written to GCF_001642675.1_ASM164267v1_genomic.fna/markers.fasta
[2024-01-24 11:51:49,475] [INFO] Task started: Blastn
[2024-01-24 11:51:49,475] [INFO] Running command: blastn -query GCF_001642675.1_ASM164267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/reference_markers.fasta -out GCF_001642675.1_ASM164267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:50,578] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:50,583] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:50,584] [INFO] Target genome list was writen to GCF_001642675.1_ASM164267v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:50,644] [INFO] Task started: fastANI
[2024-01-24 11:51:50,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg40555c0b-38af-441e-91c4-f9bc1d31b65a/GCF_001642675.1_ASM164267v1_genomic.fna.gz --refList GCF_001642675.1_ASM164267v1_genomic.fna/target_genomes.txt --output GCF_001642675.1_ASM164267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:27,972] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:27,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:27,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:27,989] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:27,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:27,990] [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 diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	100.0	3035	3035	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	99.9984	3034	3035	95	conclusive
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	93.4913	2317	3035	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	90.7947	2300	3035	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	90.6386	2283	3035	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	89.8365	2108	3035	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	89.7474	2153	3035	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.4693	1865	3035	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.375	2063	3035	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.3093	2155	3035	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	89.291	2157	3035	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	89.2367	1941	3035	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.2112	2066	3035	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.1033	1597	3035	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	83.0865	1497	3035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,992] [INFO] DFAST Taxonomy check result was written to GCF_001642675.1_ASM164267v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:27,993] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:27,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:27,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/checkm_data
[2024-01-24 11:52:27,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:28,078] [INFO] Task started: CheckM
[2024-01-24 11:52:28,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001642675.1_ASM164267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001642675.1_ASM164267v1_genomic.fna/checkm_input GCF_001642675.1_ASM164267v1_genomic.fna/checkm_result
[2024-01-24 11:53:52,337] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:52,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:52,366] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:52,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:52,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001642675.1_ASM164267v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:52,367] [INFO] Task started: Blastn
[2024-01-24 11:53:52,367] [INFO] Running command: blastn -query GCF_001642675.1_ASM164267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d6f754b-6726-4357-ba64-86341021d76b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001642675.1_ASM164267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:54,619] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:54,623] [INFO] Selected 19 target genomes.
[2024-01-24 11:53:54,623] [INFO] Target genome list was writen to GCF_001642675.1_ASM164267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:54,639] [INFO] Task started: fastANI
[2024-01-24 11:53:54,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg40555c0b-38af-441e-91c4-f9bc1d31b65a/GCF_001642675.1_ASM164267v1_genomic.fna.gz --refList GCF_001642675.1_ASM164267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001642675.1_ASM164267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:37,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:37,775] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:37,776] [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_000011365.1	s__Bradyrhizobium diazoefficiens	99.9984	3034	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	conclusive
GCF_004571025.1	s__Bradyrhizobium niftali	93.4946	2317	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	90.4541	2186	3035	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	90.4481	2127	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	90.2652	1868	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	90.0542	2180	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	89.8064	2009	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	89.7349	2155	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	89.6937	2023	3035	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	89.6162	2097	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	89.523	2176	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_015291705.1	s__Bradyrhizobium arachidis	89.3179	2153	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_007290395.1	s__Bradyrhizobium cosmicum	89.2273	1943	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.97	0.97	2	-
GCF_002795245.1	s__Bradyrhizobium forestalis	89.2155	2065	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	88.8755	1957	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	88.874	1923	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	88.5504	1991	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616425.1	s__Bradyrhizobium diazoefficiens_E	88.5425	1707	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	88.1948	1934	3035	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:37,778] [INFO] GTDB search result was written to GCF_001642675.1_ASM164267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:37,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:37,783] [INFO] DFAST_QC result json was written to GCF_001642675.1_ASM164267v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:37,783] [INFO] DFAST_QC completed!
[2024-01-24 11:54:37,783] [INFO] Total running time: 0h3m18s