[2024-01-24 15:02:33,611] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,613] [INFO] DQC Reference Directory: /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference
[2024-01-24 15:02:34,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,853] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg20c5bf39-5e04-49f1-94a0-59f7be0b3153/GCF_004114425.1_ASM411442v1_genomic.fna.gz | prodigal -d GCF_004114425.1_ASM411442v1_genomic.fna/cds.fna -a GCF_004114425.1_ASM411442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:59,674] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:59,674] [INFO] Task started: HMMsearch
[2024-01-24 15:02:59,674] [INFO] Running command: hmmsearch --tblout GCF_004114425.1_ASM411442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/reference_markers.hmm GCF_004114425.1_ASM411442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:00,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:00,143] [INFO] Found 6/6 markers.
[2024-01-24 15:03:00,214] [INFO] Query marker FASTA was written to GCF_004114425.1_ASM411442v1_genomic.fna/markers.fasta
[2024-01-24 15:03:00,214] [INFO] Task started: Blastn
[2024-01-24 15:03:00,214] [INFO] Running command: blastn -query GCF_004114425.1_ASM411442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/reference_markers.fasta -out GCF_004114425.1_ASM411442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:01,421] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:01,425] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:01,425] [INFO] Target genome list was writen to GCF_004114425.1_ASM411442v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:01,437] [INFO] Task started: fastANI
[2024-01-24 15:03:01,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg20c5bf39-5e04-49f1-94a0-59f7be0b3153/GCF_004114425.1_ASM411442v1_genomic.fna.gz --refList GCF_004114425.1_ASM411442v1_genomic.fna/target_genomes.txt --output GCF_004114425.1_ASM411442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:42,238] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:42,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:42,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:42,253] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:42,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:42,253] [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 vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	100.0	2639	2647	95	conclusive
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	91.834	1951	2647	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	89.9544	1904	2647	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	89.9357	1789	2647	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	89.918	1832	2647	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	89.6591	1866	2647	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.3153	2050	2647	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.2749	1908	2647	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.9918	1912	2647	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.9636	1843	2647	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.9363	1806	2647	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	88.7126	1902	2647	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	88.6118	1685	2647	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.341	1833	2647	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	88.3405	1803	2647	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.1357	1614	2647	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.6742	1368	2647	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.5758	1382	2647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:42,255] [INFO] DFAST Taxonomy check result was written to GCF_004114425.1_ASM411442v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:42,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:42,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:42,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/checkm_data
[2024-01-24 15:03:42,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:42,336] [INFO] Task started: CheckM
[2024-01-24 15:03:42,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004114425.1_ASM411442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004114425.1_ASM411442v1_genomic.fna/checkm_input GCF_004114425.1_ASM411442v1_genomic.fna/checkm_result
[2024-01-24 15:04:50,422] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:50,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:50,462] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:50,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:50,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004114425.1_ASM411442v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:50,464] [INFO] Task started: Blastn
[2024-01-24 15:04:50,464] [INFO] Running command: blastn -query GCF_004114425.1_ASM411442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefda6d1d-43a7-4d05-9fa9-ed9169530ae8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004114425.1_ASM411442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:52,789] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:52,795] [INFO] Selected 16 target genomes.
[2024-01-24 15:04:52,795] [INFO] Target genome list was writen to GCF_004114425.1_ASM411442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:52,805] [INFO] Task started: fastANI
[2024-01-24 15:04:52,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg20c5bf39-5e04-49f1-94a0-59f7be0b3153/GCF_004114425.1_ASM411442v1_genomic.fna.gz --refList GCF_004114425.1_ASM411442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004114425.1_ASM411442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:27,804] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:27,817] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:27,817] [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_004114425.1	s__Bradyrhizobium vignae	100.0	2639	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.81	0.88	0.86	3	conclusive
GCF_000473065.1	s__Bradyrhizobium sp000473065	92.0036	1980	2647	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	92.0002	1766	2647	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	91.8289	1951	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291725.1	s__Bradyrhizobium japonicum_D	90.1515	1893	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	90.1333	1920	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	90.0376	1772	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031625.1	s__Bradyrhizobium agreste	89.9547	1904	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031655.1	s__Bradyrhizobium glycinis	89.9101	1833	2647	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	89.8267	1824	2647	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	89.763	1901	2647	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	89.7178	1795	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094575.1	s__Bradyrhizobium yuanmingense	89.6715	1864	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	95.91	0.89	0.81	9	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	89.5494	1782	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556045.1	s__Bradyrhizobium sp001556045	89.5218	1674	2647	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	89.2983	1905	2647	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:27,830] [INFO] GTDB search result was written to GCF_004114425.1_ASM411442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:27,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:27,837] [INFO] DFAST_QC result json was written to GCF_004114425.1_ASM411442v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:27,837] [INFO] DFAST_QC completed!
[2024-01-24 15:05:27,837] [INFO] Total running time: 0h2m54s