[2024-01-24 15:26:40,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:40,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:40,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference
[2024-01-24 15:26:41,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,635] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg114ff55d-ba7e-45ec-96db-6fb1a86bb2ce/GCF_027594865.1_ASM2759486v1_genomic.fna.gz | prodigal -d GCF_027594865.1_ASM2759486v1_genomic.fna/cds.fna -a GCF_027594865.1_ASM2759486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:07,053] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:07,053] [INFO] Task started: HMMsearch
[2024-01-24 15:27:07,053] [INFO] Running command: hmmsearch --tblout GCF_027594865.1_ASM2759486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/reference_markers.hmm GCF_027594865.1_ASM2759486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:07,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:07,447] [INFO] Found 6/6 markers.
[2024-01-24 15:27:07,510] [INFO] Query marker FASTA was written to GCF_027594865.1_ASM2759486v1_genomic.fna/markers.fasta
[2024-01-24 15:27:07,510] [INFO] Task started: Blastn
[2024-01-24 15:27:07,511] [INFO] Running command: blastn -query GCF_027594865.1_ASM2759486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/reference_markers.fasta -out GCF_027594865.1_ASM2759486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:08,704] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:08,708] [INFO] Selected 23 target genomes.
[2024-01-24 15:27:08,709] [INFO] Target genome list was writen to GCF_027594865.1_ASM2759486v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:08,718] [INFO] Task started: fastANI
[2024-01-24 15:27:08,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg114ff55d-ba7e-45ec-96db-6fb1a86bb2ce/GCF_027594865.1_ASM2759486v1_genomic.fna.gz --refList GCF_027594865.1_ASM2759486v1_genomic.fna/target_genomes.txt --output GCF_027594865.1_ASM2759486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:59,322] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:59,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:59,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:59,342] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:59,343] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:59,343] [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 japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	90.1082	2055	2758	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	90.0861	2018	2758	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	90.0721	2048	2758	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.5602	2070	2758	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	89.5507	1828	2758	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.4943	2079	2758	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.4565	1822	2758	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.4507	2078	2758	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.4373	2037	2758	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.3691	2037	2758	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.2469	1978	2758	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	89.1867	1920	2758	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	89.1854	1939	2758	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	89.1578	1852	2758	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	89.1023	1876	2758	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	88.9997	1934	2758	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.8199	1911	2758	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	88.817	2026	2758	95	below_threshold
Bradyrhizobium canariense	strain=BTA-1	GCA_019402665.1	255045	255045	suspected-type	True	88.7264	1926	2758	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.4424	1900	2758	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	88.2734	1956	2758	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	83.1383	1544	2758	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9594	1514	2758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:59,345] [INFO] DFAST Taxonomy check result was written to GCF_027594865.1_ASM2759486v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:59,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:59,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:59,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/checkm_data
[2024-01-24 15:27:59,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:59,427] [INFO] Task started: CheckM
[2024-01-24 15:27:59,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027594865.1_ASM2759486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027594865.1_ASM2759486v1_genomic.fna/checkm_input GCF_027594865.1_ASM2759486v1_genomic.fna/checkm_result
[2024-01-24 15:29:16,167] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:16,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:16,204] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:16,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:16,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027594865.1_ASM2759486v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:16,206] [INFO] Task started: Blastn
[2024-01-24 15:29:16,206] [INFO] Running command: blastn -query GCF_027594865.1_ASM2759486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb921cf10-d3f8-409b-8f0b-2033ee2081d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_027594865.1_ASM2759486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:18,478] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:18,482] [INFO] Selected 25 target genomes.
[2024-01-24 15:29:18,483] [INFO] Target genome list was writen to GCF_027594865.1_ASM2759486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:18,501] [INFO] Task started: fastANI
[2024-01-24 15:29:18,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg114ff55d-ba7e-45ec-96db-6fb1a86bb2ce/GCF_027594865.1_ASM2759486v1_genomic.fna.gz --refList GCF_027594865.1_ASM2759486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027594865.1_ASM2759486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:11,780] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:11,803] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:30:11,803] [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_018130785.1	s__Bradyrhizobium liaoningense_A	90.1664	1994	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284375.1	s__Bradyrhizobium japonicum	90.0737	2061	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	90.0534	2037	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_004123905.1	s__Bradyrhizobium betae_A	89.8749	2064	2758	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	89.8383	1868	2758	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	89.6493	2038	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008932115.1	s__Bradyrhizobium betae	89.5561	1827	2758	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	89.5445	2004	2758	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	89.5246	2024	2758	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	89.4602	2035	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.4499	2077	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_002278135.2	s__Bradyrhizobium ottawaense	89.4477	2035	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	89.4412	2016	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	89.4284	1935	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094605.1	s__Bradyrhizobium shewense	89.3762	2036	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.2138	1867	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007290395.1	s__Bradyrhizobium cosmicum	89.1818	1921	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.97	0.97	2	-
GCF_002266465.2	s__Bradyrhizobium symbiodeficiens	89.1737	1850	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	89.1719	1941	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_002266435.2	s__Bradyrhizobium amphicarpaeae	89.106	1875	2758	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	89.0161	1932	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	88.8886	1874	2758	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	88.8002	1877	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473045.1	s__Bradyrhizobium sp000473045	88.647	1982	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129965.1	s__Bradyrhizobium diazoefficiens_A	88.3137	1721	2758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.99	99.99	0.99	0.99	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:11,805] [INFO] GTDB search result was written to GCF_027594865.1_ASM2759486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:11,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:11,810] [INFO] DFAST_QC result json was written to GCF_027594865.1_ASM2759486v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:11,810] [INFO] DFAST_QC completed!
[2024-01-24 15:30:11,810] [INFO] Total running time: 0h3m31s