[2024-01-24 15:02:03,509] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference
[2024-01-24 15:02:06,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,126] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6977823-351e-414e-b87e-52d0d6738b18/GCF_016031625.1_ASM1603162v1_genomic.fna.gz | prodigal -d GCF_016031625.1_ASM1603162v1_genomic.fna/cds.fna -a GCF_016031625.1_ASM1603162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:29,707] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:29,707] [INFO] Task started: HMMsearch
[2024-01-24 15:02:29,708] [INFO] Running command: hmmsearch --tblout GCF_016031625.1_ASM1603162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/reference_markers.hmm GCF_016031625.1_ASM1603162v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:30,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:30,063] [INFO] Found 6/6 markers.
[2024-01-24 15:02:30,128] [INFO] Query marker FASTA was written to GCF_016031625.1_ASM1603162v1_genomic.fna/markers.fasta
[2024-01-24 15:02:30,129] [INFO] Task started: Blastn
[2024-01-24 15:02:30,129] [INFO] Running command: blastn -query GCF_016031625.1_ASM1603162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/reference_markers.fasta -out GCF_016031625.1_ASM1603162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:31,218] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:31,242] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:31,242] [INFO] Target genome list was writen to GCF_016031625.1_ASM1603162v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:31,262] [INFO] Task started: fastANI
[2024-01-24 15:02:31,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6977823-351e-414e-b87e-52d0d6738b18/GCF_016031625.1_ASM1603162v1_genomic.fna.gz --refList GCF_016031625.1_ASM1603162v1_genomic.fna/target_genomes.txt --output GCF_016031625.1_ASM1603162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:10,308] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:10,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:10,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:10,323] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:10,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:10,323] [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 agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	100.0	2590	2591	95	conclusive
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	93.9209	2040	2591	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	92.6997	2005	2591	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	90.7101	1985	2591	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	89.9815	1898	2591	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.2742	2039	2591	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.2604	1952	2591	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.1585	1822	2591	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.9314	1927	2591	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.7522	1957	2591	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	88.676	1937	2591	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.6591	1911	2591	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.6364	1890	2591	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.5536	1748	2591	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.0983	1629	2591	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.8803	1454	2591	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8542	1370	2591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:10,325] [INFO] DFAST Taxonomy check result was written to GCF_016031625.1_ASM1603162v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:10,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:10,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:10,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/checkm_data
[2024-01-24 15:03:10,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:10,405] [INFO] Task started: CheckM
[2024-01-24 15:03:10,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016031625.1_ASM1603162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016031625.1_ASM1603162v1_genomic.fna/checkm_input GCF_016031625.1_ASM1603162v1_genomic.fna/checkm_result
[2024-01-24 15:04:18,898] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:18,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:18,926] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:18,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:18,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016031625.1_ASM1603162v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:18,928] [INFO] Task started: Blastn
[2024-01-24 15:04:18,928] [INFO] Running command: blastn -query GCF_016031625.1_ASM1603162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd23cc7ea-5c81-4202-a934-e0a4fc1b1136/dqc_reference/reference_markers_gtdb.fasta -out GCF_016031625.1_ASM1603162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:21,219] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:21,222] [INFO] Selected 10 target genomes.
[2024-01-24 15:04:21,223] [INFO] Target genome list was writen to GCF_016031625.1_ASM1603162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:21,229] [INFO] Task started: fastANI
[2024-01-24 15:04:21,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6977823-351e-414e-b87e-52d0d6738b18/GCF_016031625.1_ASM1603162v1_genomic.fna.gz --refList GCF_016031625.1_ASM1603162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016031625.1_ASM1603162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:47,175] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:47,188] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:47,189] [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_016031625.1	s__Bradyrhizobium agreste	100.0	2590	2591	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_016031655.1	s__Bradyrhizobium glycinis	93.9114	2041	2591	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	92.7087	2004	2591	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	92.627	2049	2591	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	92.5479	1894	2591	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	91.2686	2051	2591	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	91.2197	1814	2591	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	90.7213	1983	2591	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	89.4716	1842	2591	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	89.2702	1950	2591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:47,190] [INFO] GTDB search result was written to GCF_016031625.1_ASM1603162v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:47,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:47,194] [INFO] DFAST_QC result json was written to GCF_016031625.1_ASM1603162v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:47,195] [INFO] DFAST_QC completed!
[2024-01-24 15:04:47,195] [INFO] Total running time: 0h2m44s