[2024-01-25 18:03:36,083] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:36,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:36,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference
[2024-01-25 18:03:37,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:37,230] [INFO] Task started: Prodigal
[2024-01-25 18:03:37,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg9446de24-94f9-44fe-b418-97a85114e37c/GCF_014529705.1_ASM1452970v1_genomic.fna.gz | prodigal -d GCF_014529705.1_ASM1452970v1_genomic.fna/cds.fna -a GCF_014529705.1_ASM1452970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:00,757] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:00,757] [INFO] Task started: HMMsearch
[2024-01-25 18:04:00,757] [INFO] Running command: hmmsearch --tblout GCF_014529705.1_ASM1452970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/reference_markers.hmm GCF_014529705.1_ASM1452970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:01,091] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:01,092] [INFO] Found 6/6 markers.
[2024-01-25 18:04:01,157] [INFO] Query marker FASTA was written to GCF_014529705.1_ASM1452970v1_genomic.fna/markers.fasta
[2024-01-25 18:04:01,158] [INFO] Task started: Blastn
[2024-01-25 18:04:01,158] [INFO] Running command: blastn -query GCF_014529705.1_ASM1452970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/reference_markers.fasta -out GCF_014529705.1_ASM1452970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:02,099] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:02,103] [INFO] Selected 26 target genomes.
[2024-01-25 18:04:02,103] [INFO] Target genome list was writen to GCF_014529705.1_ASM1452970v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:02,131] [INFO] Task started: fastANI
[2024-01-25 18:04:02,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg9446de24-94f9-44fe-b418-97a85114e37c/GCF_014529705.1_ASM1452970v1_genomic.fna.gz --refList GCF_014529705.1_ASM1452970v1_genomic.fna/target_genomes.txt --output GCF_014529705.1_ASM1452970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:56,556] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:56,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:56,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:56,574] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:56,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:56,574] [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 campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	100.0	2902	2912	95	conclusive
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	88.9497	1844	2912	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	88.9229	1881	2912	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	88.841	1978	2912	95	below_threshold
Bradyrhizobium guangdongense	strain=CGMCC 1.15034	GCA_014640515.1	1325090	1325090	type	True	88.7436	1908	2912	95	below_threshold
Bradyrhizobium guangdongense	strain=CCBAU 51649	GCA_004114975.1	1325090	1325090	type	True	88.7267	1931	2912	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	88.6662	1867	2912	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.0468	1896	2912	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	87.9913	1915	2912	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	87.9774	1931	2912	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	87.9618	1920	2912	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	87.8472	1871	2912	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	87.795	1784	2912	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	87.6861	1894	2912	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	87.5552	1788	2912	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	87.5098	1797	2912	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	87.427	1833	2912	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	87.3657	1815	2912	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	87.3483	1787	2912	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	87.0839	1795	2912	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	87.0458	1779	2912	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.782	1455	2912	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.6314	1371	2912	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	82.6254	1370	2912	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	78.0645	434	2912	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	76.7104	343	2912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:56,576] [INFO] DFAST Taxonomy check result was written to GCF_014529705.1_ASM1452970v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:56,576] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:56,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:56,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/checkm_data
[2024-01-25 18:04:56,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:56,662] [INFO] Task started: CheckM
[2024-01-25 18:04:56,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014529705.1_ASM1452970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014529705.1_ASM1452970v1_genomic.fna/checkm_input GCF_014529705.1_ASM1452970v1_genomic.fna/checkm_result
[2024-01-25 18:06:06,880] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:06,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:06,905] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:06,905] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:06,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014529705.1_ASM1452970v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:06,908] [INFO] Task started: Blastn
[2024-01-25 18:06:06,908] [INFO] Running command: blastn -query GCF_014529705.1_ASM1452970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77badd82-db44-4596-bd41-06b07d5a3554/dqc_reference/reference_markers_gtdb.fasta -out GCF_014529705.1_ASM1452970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:08,789] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:08,792] [INFO] Selected 21 target genomes.
[2024-01-25 18:06:08,792] [INFO] Target genome list was writen to GCF_014529705.1_ASM1452970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:08,824] [INFO] Task started: fastANI
[2024-01-25 18:06:08,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg9446de24-94f9-44fe-b418-97a85114e37c/GCF_014529705.1_ASM1452970v1_genomic.fna.gz --refList GCF_014529705.1_ASM1452970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014529705.1_ASM1452970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:50,195] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:50,209] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:50,210] [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_014529705.1	s__Bradyrhizobium campsiandrae	100.0	2903	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_015291645.1	s__Bradyrhizobium sp015291645	90.0391	1940	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291665.1	s__Bradyrhizobium sp015291665	89.11	1822	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872875.1	s__Bradyrhizobium sp017872875	89.0229	1896	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440035.1	s__Bradyrhizobium manausense	88.9542	1842	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114955.1	s__Bradyrhizobium guangzhouense	88.9176	1882	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
GCF_000473045.1	s__Bradyrhizobium sp000473045	88.7371	1870	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115265.1	s__Bradyrhizobium sp900115265	88.5556	1800	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129685.1	s__Bradyrhizobium manausense_D	88.4791	1884	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113735.1	s__Bradyrhizobium sp900113735	88.1477	1704	2912	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	88.122	1889	2912	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	88.0686	1891	2912	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	87.9833	1916	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	87.9583	1921	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_004571025.1	s__Bradyrhizobium niftali	87.8607	1869	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	87.6724	1789	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	87.6659	1898	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_015291725.1	s__Bradyrhizobium japonicum_D	87.2324	1835	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCA_008933495.1	s__Pseudorhodoplanes sp008933495	78.1323	292	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	76.8085	251	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_014359905.1	s__Hoeflea sp014359905	76.7539	295	2912	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:50,211] [INFO] GTDB search result was written to GCF_014529705.1_ASM1452970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:50,212] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:50,216] [INFO] DFAST_QC result json was written to GCF_014529705.1_ASM1452970v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:50,216] [INFO] DFAST_QC completed!
[2024-01-25 18:06:50,216] [INFO] Total running time: 0h3m14s