[2024-01-25 18:55:50,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:50,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:50,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference
[2024-01-25 18:55:51,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:51,765] [INFO] Task started: Prodigal
[2024-01-25 18:55:51,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg692ec8b0-ca87-423a-8211-add5fd86c1f8/GCF_024806875.1_ASM2480687v1_genomic.fna.gz | prodigal -d GCF_024806875.1_ASM2480687v1_genomic.fna/cds.fna -a GCF_024806875.1_ASM2480687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:11,062] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:11,062] [INFO] Task started: HMMsearch
[2024-01-25 18:56:11,062] [INFO] Running command: hmmsearch --tblout GCF_024806875.1_ASM2480687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/reference_markers.hmm GCF_024806875.1_ASM2480687v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:11,378] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:11,379] [INFO] Found 6/6 markers.
[2024-01-25 18:56:11,435] [INFO] Query marker FASTA was written to GCF_024806875.1_ASM2480687v1_genomic.fna/markers.fasta
[2024-01-25 18:56:11,435] [INFO] Task started: Blastn
[2024-01-25 18:56:11,435] [INFO] Running command: blastn -query GCF_024806875.1_ASM2480687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/reference_markers.fasta -out GCF_024806875.1_ASM2480687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:12,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:12,382] [INFO] Selected 19 target genomes.
[2024-01-25 18:56:12,382] [INFO] Target genome list was writen to GCF_024806875.1_ASM2480687v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:12,440] [INFO] Task started: fastANI
[2024-01-25 18:56:12,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg692ec8b0-ca87-423a-8211-add5fd86c1f8/GCF_024806875.1_ASM2480687v1_genomic.fna.gz --refList GCF_024806875.1_ASM2480687v1_genomic.fna/target_genomes.txt --output GCF_024806875.1_ASM2480687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:47,416] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:47,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:47,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:47,428] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:56:47,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:47,429] [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 betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	100.0	2430	2431	95	conclusive
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	99.9981	2431	2431	95	conclusive
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	94.11	1962	2431	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	89.6898	1816	2431	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.6836	1838	2431	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	89.6652	1838	2431	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.5937	1841	2431	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.479	1784	2431	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	89.018	1779	2431	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.9195	1841	2431	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.8693	1761	2431	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	88.7661	1839	2431	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	87.9921	1699	2431	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9581	1399	2431	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.8045	1322	2431	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	78.0446	514	2431	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	77.2091	362	2431	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	76.2602	153	2431	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	76.1886	151	2431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:47,430] [INFO] DFAST Taxonomy check result was written to GCF_024806875.1_ASM2480687v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:47,430] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:47,431] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:47,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/checkm_data
[2024-01-25 18:56:47,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:47,499] [INFO] Task started: CheckM
[2024-01-25 18:56:47,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024806875.1_ASM2480687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024806875.1_ASM2480687v1_genomic.fna/checkm_input GCF_024806875.1_ASM2480687v1_genomic.fna/checkm_result
[2024-01-25 18:57:42,025] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:42,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:42,055] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:42,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:42,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024806875.1_ASM2480687v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:42,057] [INFO] Task started: Blastn
[2024-01-25 18:57:42,057] [INFO] Running command: blastn -query GCF_024806875.1_ASM2480687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c314ba7-7daa-44e4-826f-2934298f65a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024806875.1_ASM2480687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:43,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:43,893] [INFO] Selected 21 target genomes.
[2024-01-25 18:57:43,893] [INFO] Target genome list was writen to GCF_024806875.1_ASM2480687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:43,916] [INFO] Task started: fastANI
[2024-01-25 18:57:43,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg692ec8b0-ca87-423a-8211-add5fd86c1f8/GCF_024806875.1_ASM2480687v1_genomic.fna.gz --refList GCF_024806875.1_ASM2480687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024806875.1_ASM2480687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:26,766] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:26,779] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:26,779] [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_008932115.1	s__Bradyrhizobium betae	99.9981	2431	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007290395.1	s__Bradyrhizobium cosmicum	94.1	1963	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.97	0.97	2	-
GCF_018129965.1	s__Bradyrhizobium diazoefficiens_A	90.4032	1796	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.99	99.99	0.99	0.99	8	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	89.7196	1810	2431	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	89.6844	1841	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	89.6785	1729	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.5979	1840	2431	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	89.4905	1783	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	89.3664	1766	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266465.2	s__Bradyrhizobium symbiodeficiens	89.0031	1781	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	-
GCF_002266435.2	s__Bradyrhizobium amphicarpaeae	88.9155	1842	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	88.8192	1779	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	88.7958	1835	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_000938255.1	s__Bradyrhizobium sp000938255	88.5331	1752	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	88.2355	1718	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	88.1655	1725	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612535.1	s__Bradyrhizobium diazoefficiens_C	88.0767	1688	2431	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	87.7701	1760	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	83.0808	1398	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_000314735.2	s__Afipia felis	79.9344	588	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.60	95.79	0.96	0.87	4	-
GCA_017308135.1	s__Tagaea sp017308135	77.5282	297	2431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	97.31	97.31	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:26,781] [INFO] GTDB search result was written to GCF_024806875.1_ASM2480687v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:26,781] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:26,784] [INFO] DFAST_QC result json was written to GCF_024806875.1_ASM2480687v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:26,785] [INFO] DFAST_QC completed!
[2024-01-25 18:58:26,785] [INFO] Total running time: 0h2m36s