[2024-01-25 19:54:50,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:50,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:50,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference
[2024-01-25 19:54:51,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:51,947] [INFO] Task started: Prodigal
[2024-01-25 19:54:51,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fc2454c-4033-405b-8962-6b17d75ae957/GCF_020889685.1_ASM2088968v1_genomic.fna.gz | prodigal -d GCF_020889685.1_ASM2088968v1_genomic.fna/cds.fna -a GCF_020889685.1_ASM2088968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:14,186] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:14,186] [INFO] Task started: HMMsearch
[2024-01-25 19:55:14,186] [INFO] Running command: hmmsearch --tblout GCF_020889685.1_ASM2088968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/reference_markers.hmm GCF_020889685.1_ASM2088968v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:14,524] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:14,526] [INFO] Found 6/6 markers.
[2024-01-25 19:55:14,592] [INFO] Query marker FASTA was written to GCF_020889685.1_ASM2088968v1_genomic.fna/markers.fasta
[2024-01-25 19:55:14,592] [INFO] Task started: Blastn
[2024-01-25 19:55:14,592] [INFO] Running command: blastn -query GCF_020889685.1_ASM2088968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/reference_markers.fasta -out GCF_020889685.1_ASM2088968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:15,522] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:15,527] [INFO] Selected 18 target genomes.
[2024-01-25 19:55:15,527] [INFO] Target genome list was writen to GCF_020889685.1_ASM2088968v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:15,533] [INFO] Task started: fastANI
[2024-01-25 19:55:15,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc2454c-4033-405b-8962-6b17d75ae957/GCF_020889685.1_ASM2088968v1_genomic.fna.gz --refList GCF_020889685.1_ASM2088968v1_genomic.fna/target_genomes.txt --output GCF_020889685.1_ASM2088968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:50,584] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:50,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:50,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:50,595] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:55:50,596] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:55:50,596] [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 oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	100.0	2761	2774	95	inconclusive
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	95.1122	2061	2774	95	inconclusive
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	95.0465	2094	2774	95	inconclusive
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	92.6608	2201	2774	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	91.1339	1995	2774	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	91.0854	2098	2774	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	90.7948	2156	2774	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	90.734	2068	2774	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.6441	2053	2774	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	90.6407	1999	2774	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.6261	2067	2774	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	90.0594	2052	2774	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	82.5042	1383	2774	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	79.5371	544	2774	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.0242	381	2774	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	76.9404	298	2774	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	76.875	298	2774	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.585	203	2774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:50,597] [INFO] DFAST Taxonomy check result was written to GCF_020889685.1_ASM2088968v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:50,598] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:50,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:50,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/checkm_data
[2024-01-25 19:55:50,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:50,692] [INFO] Task started: CheckM
[2024-01-25 19:55:50,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020889685.1_ASM2088968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020889685.1_ASM2088968v1_genomic.fna/checkm_input GCF_020889685.1_ASM2088968v1_genomic.fna/checkm_result
[2024-01-25 19:56:54,073] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:54,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:54,093] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:54,093] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:54,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020889685.1_ASM2088968v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:54,094] [INFO] Task started: Blastn
[2024-01-25 19:56:54,094] [INFO] Running command: blastn -query GCF_020889685.1_ASM2088968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg362e1a40-5f9f-4364-8d1b-dd999bb7a182/dqc_reference/reference_markers_gtdb.fasta -out GCF_020889685.1_ASM2088968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:55,928] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:55,931] [INFO] Selected 26 target genomes.
[2024-01-25 19:56:55,931] [INFO] Target genome list was writen to GCF_020889685.1_ASM2088968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:55,952] [INFO] Task started: fastANI
[2024-01-25 19:56:55,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc2454c-4033-405b-8962-6b17d75ae957/GCF_020889685.1_ASM2088968v1_genomic.fna.gz --refList GCF_020889685.1_ASM2088968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020889685.1_ASM2088968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:42,670] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:42,685] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:57:42,685] [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
GCF_018130545.1	s__Bradyrhizobium tropiciagri_A	91.6218	2001	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	91.5876	2075	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_013373795.1	s__Bradyrhizobium quebecense	91.1864	2076	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_003001755.1	s__Bradyrhizobium sp003001755	91.1679	1894	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	91.1527	2180	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982635.1	s__Bradyrhizobium mercantei	91.144	1993	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002532045.1	s__Bradyrhizobium sp002532045	91.0485	2080	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	90.9569	2120	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	90.9354	2005	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	90.7808	2158	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	90.7159	2070	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_000379145.1	s__Bradyrhizobium elkanii	90.6468	2064	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	90.6415	1953	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	90.6307	2001	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	90.1317	2023	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
GCF_002831585.1	s__Bradyrhizobium sp002831585	90.0289	1899	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.70	98.62	0.95	0.93	5	-
GCF_014529705.1	s__Bradyrhizobium campsiandrae	82.4984	1385	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000218565.1	s__Afipia carboxidovorans	79.5325	544	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.99	99.99	1.00	1.00	3	-
GCF_016756535.1	s__Mesorhizobium sp016756535	77.4705	445	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	77.391	424	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842935.1	s__DUSC01 sp012842935	77.3319	249	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.1352	448	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCA_905339215.1	s__DUSC01 sp008933895	77.0186	361	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_018829385.1	s__Hoeflea sp018829385	76.8279	168	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469955.1	s__Neorhizobium sp900469955	76.4346	223	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642895.1	s__Roseitalea sp017642895	76.4121	222	2774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:42,692] [INFO] GTDB search result was written to GCF_020889685.1_ASM2088968v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:42,692] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:42,696] [INFO] DFAST_QC result json was written to GCF_020889685.1_ASM2088968v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:42,696] [INFO] DFAST_QC completed!
[2024-01-25 19:57:42,696] [INFO] Total running time: 0h2m52s