[2024-01-25 19:32:36,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:36,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:36,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference
[2024-01-25 19:32:37,702] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:37,703] [INFO] Task started: Prodigal
[2024-01-25 19:32:37,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg86340f63-e99d-45b6-9dd7-0a84f71da791/GCF_016031655.1_ASM1603165v1_genomic.fna.gz | prodigal -d GCF_016031655.1_ASM1603165v1_genomic.fna/cds.fna -a GCF_016031655.1_ASM1603165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:57,932] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:57,933] [INFO] Task started: HMMsearch
[2024-01-25 19:32:57,933] [INFO] Running command: hmmsearch --tblout GCF_016031655.1_ASM1603165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/reference_markers.hmm GCF_016031655.1_ASM1603165v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:58,211] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:58,212] [INFO] Found 6/6 markers.
[2024-01-25 19:32:58,268] [INFO] Query marker FASTA was written to GCF_016031655.1_ASM1603165v1_genomic.fna/markers.fasta
[2024-01-25 19:32:58,269] [INFO] Task started: Blastn
[2024-01-25 19:32:58,269] [INFO] Running command: blastn -query GCF_016031655.1_ASM1603165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/reference_markers.fasta -out GCF_016031655.1_ASM1603165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:59,253] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:59,255] [INFO] Selected 16 target genomes.
[2024-01-25 19:32:59,256] [INFO] Target genome list was writen to GCF_016031655.1_ASM1603165v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:59,260] [INFO] Task started: fastANI
[2024-01-25 19:32:59,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg86340f63-e99d-45b6-9dd7-0a84f71da791/GCF_016031655.1_ASM1603165v1_genomic.fna.gz --refList GCF_016031655.1_ASM1603165v1_genomic.fna/target_genomes.txt --output GCF_016031655.1_ASM1603165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:34,388] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:34,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:34,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:34,401] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:34,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:34,401] [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 glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	100.0	2557	2561	95	conclusive
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	94.0101	2040	2561	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	93.4895	2021	2561	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	90.567	1942	2561	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	90.1153	1863	2561	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	89.8758	1839	2561	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.2713	1854	2561	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.0619	1964	2561	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	88.7983	1954	2561	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	88.6545	1936	2561	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.5712	1902	2561	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.5388	1898	2561	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.4099	1979	2561	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.0774	1644	2561	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8111	1355	2561	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.7832	1462	2561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:34,403] [INFO] DFAST Taxonomy check result was written to GCF_016031655.1_ASM1603165v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:34,403] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:34,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:34,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/checkm_data
[2024-01-25 19:33:34,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:34,476] [INFO] Task started: CheckM
[2024-01-25 19:33:34,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016031655.1_ASM1603165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016031655.1_ASM1603165v1_genomic.fna/checkm_input GCF_016031655.1_ASM1603165v1_genomic.fna/checkm_result
[2024-01-25 19:34:32,348] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:32,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:32,368] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:32,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:32,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016031655.1_ASM1603165v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:32,369] [INFO] Task started: Blastn
[2024-01-25 19:34:32,369] [INFO] Running command: blastn -query GCF_016031655.1_ASM1603165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2cf9408-b6c7-4017-9a60-983219fc6d67/dqc_reference/reference_markers_gtdb.fasta -out GCF_016031655.1_ASM1603165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:34,484] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:34,487] [INFO] Selected 11 target genomes.
[2024-01-25 19:34:34,487] [INFO] Target genome list was writen to GCF_016031655.1_ASM1603165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:34,494] [INFO] Task started: fastANI
[2024-01-25 19:34:34,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg86340f63-e99d-45b6-9dd7-0a84f71da791/GCF_016031655.1_ASM1603165v1_genomic.fna.gz --refList GCF_016031655.1_ASM1603165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016031655.1_ASM1603165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:00,123] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:00,130] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:00,131] [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_016031655.1	s__Bradyrhizobium glycinis	100.0	2557	2561	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_016031625.1	s__Bradyrhizobium agreste	94.0101	2040	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094575.1	s__Bradyrhizobium yuanmingense	93.4968	2020	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	95.91	0.89	0.81	9	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	93.0433	2015	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	92.8971	1948	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	91.3446	1854	2561	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	90.5761	1941	2561	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	90.5738	1945	2561	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	89.5293	1862	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	89.206	1963	2561	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	89.069	1963	2561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:00,132] [INFO] GTDB search result was written to GCF_016031655.1_ASM1603165v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:00,133] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:00,135] [INFO] DFAST_QC result json was written to GCF_016031655.1_ASM1603165v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:00,136] [INFO] DFAST_QC completed!
[2024-01-25 19:35:00,136] [INFO] Total running time: 0h2m24s