[2024-01-24 11:12:24,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference
[2024-01-24 11:12:27,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,098] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7eb6cbf-8e01-4912-a4a4-035a9f872944/GCF_008932115.1_ASM893211v1_genomic.fna.gz | prodigal -d GCF_008932115.1_ASM893211v1_genomic.fna/cds.fna -a GCF_008932115.1_ASM893211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:49,212] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:49,213] [INFO] Task started: HMMsearch
[2024-01-24 11:12:49,213] [INFO] Running command: hmmsearch --tblout GCF_008932115.1_ASM893211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/reference_markers.hmm GCF_008932115.1_ASM893211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:49,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:49,665] [INFO] Found 6/6 markers.
[2024-01-24 11:12:49,723] [INFO] Query marker FASTA was written to GCF_008932115.1_ASM893211v1_genomic.fna/markers.fasta
[2024-01-24 11:12:49,723] [INFO] Task started: Blastn
[2024-01-24 11:12:49,723] [INFO] Running command: blastn -query GCF_008932115.1_ASM893211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/reference_markers.fasta -out GCF_008932115.1_ASM893211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:50,729] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:50,733] [INFO] Selected 19 target genomes.
[2024-01-24 11:12:50,733] [INFO] Target genome list was writen to GCF_008932115.1_ASM893211v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:50,739] [INFO] Task started: fastANI
[2024-01-24 11:12:50,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7eb6cbf-8e01-4912-a4a4-035a9f872944/GCF_008932115.1_ASM893211v1_genomic.fna.gz --refList GCF_008932115.1_ASM893211v1_genomic.fna/target_genomes.txt --output GCF_008932115.1_ASM893211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:27,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:27,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:27,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:27,348] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:27,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:27,349] [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=PL7HG1	GCA_008932115.1	244734	244734	type	True	100.0	2467	2472	95	conclusive
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	99.9902	2429	2472	95	conclusive
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	94.1624	1963	2472	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	89.7334	1825	2472	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	89.7136	1857	2472	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.6628	1847	2472	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.616	1850	2472	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.5226	1778	2472	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	89.0369	1794	2472	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.9371	1825	2472	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.8518	1765	2472	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	88.8495	1828	2472	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.1092	1712	2472	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.0845	1388	2472	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.8784	1314	2472	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	77.8513	534	2472	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	77.0455	369	2472	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	76.2882	159	2472	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	76.1527	153	2472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:27,351] [INFO] DFAST Taxonomy check result was written to GCF_008932115.1_ASM893211v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:27,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:27,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:27,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/checkm_data
[2024-01-24 11:13:27,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:27,420] [INFO] Task started: CheckM
[2024-01-24 11:13:27,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008932115.1_ASM893211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008932115.1_ASM893211v1_genomic.fna/checkm_input GCF_008932115.1_ASM893211v1_genomic.fna/checkm_result
[2024-01-24 11:14:31,750] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:31,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:31,776] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:31,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:31,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008932115.1_ASM893211v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:31,777] [INFO] Task started: Blastn
[2024-01-24 11:14:31,777] [INFO] Running command: blastn -query GCF_008932115.1_ASM893211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd912417-fe28-495d-bec1-5b7bcd83eda7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008932115.1_ASM893211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:33,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:33,607] [INFO] Selected 21 target genomes.
[2024-01-24 11:14:33,607] [INFO] Target genome list was writen to GCF_008932115.1_ASM893211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:33,656] [INFO] Task started: fastANI
[2024-01-24 11:14:33,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7eb6cbf-8e01-4912-a4a4-035a9f872944/GCF_008932115.1_ASM893211v1_genomic.fna.gz --refList GCF_008932115.1_ASM893211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008932115.1_ASM893211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:15,295] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:15,312] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:15,312] [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	100.0	2468	2472	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	94.1655	1962	2472	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	90.4483	1810	2472	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	89.6943	1817	2472	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	89.6381	1851	2472	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	89.619	1739	2472	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	89.6078	1851	2472	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	89.5156	1779	2472	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	89.3622	1774	2472	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	89.0357	1794	2472	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	88.9411	1824	2472	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	88.8416	1807	2472	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	88.8394	1830	2472	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	88.4246	1789	2472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	88.2794	1737	2472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	88.1985	1723	2472	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	88.0386	1724	2472	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	87.7547	1771	2472	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	83.1427	1411	2472	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	80.0069	581	2472	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	77.503	302	2472	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:15,314] [INFO] GTDB search result was written to GCF_008932115.1_ASM893211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:15,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:15,319] [INFO] DFAST_QC result json was written to GCF_008932115.1_ASM893211v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:15,319] [INFO] DFAST_QC completed!
[2024-01-24 11:15:15,319] [INFO] Total running time: 0h2m51s