[2024-01-24 14:32:30,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference
[2024-01-24 14:32:31,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,978] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,978] [INFO] Running command: gunzip -c /var/lib/cwl/stga784ec81-51e8-4fb2-a5a2-6d9fc2a9109d/GCF_018736085.1_ASM1873608v1_genomic.fna.gz | prodigal -d GCF_018736085.1_ASM1873608v1_genomic.fna/cds.fna -a GCF_018736085.1_ASM1873608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:48,695] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:48,696] [INFO] Task started: HMMsearch
[2024-01-24 14:32:48,696] [INFO] Running command: hmmsearch --tblout GCF_018736085.1_ASM1873608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/reference_markers.hmm GCF_018736085.1_ASM1873608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:49,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:49,057] [INFO] Found 6/6 markers.
[2024-01-24 14:32:49,118] [INFO] Query marker FASTA was written to GCF_018736085.1_ASM1873608v1_genomic.fna/markers.fasta
[2024-01-24 14:32:49,119] [INFO] Task started: Blastn
[2024-01-24 14:32:49,119] [INFO] Running command: blastn -query GCF_018736085.1_ASM1873608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/reference_markers.fasta -out GCF_018736085.1_ASM1873608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:50,159] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:50,163] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:50,164] [INFO] Target genome list was writen to GCF_018736085.1_ASM1873608v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:50,172] [INFO] Task started: fastANI
[2024-01-24 14:32:50,172] [INFO] Running command: fastANI --query /var/lib/cwl/stga784ec81-51e8-4fb2-a5a2-6d9fc2a9109d/GCF_018736085.1_ASM1873608v1_genomic.fna.gz --refList GCF_018736085.1_ASM1873608v1_genomic.fna/target_genomes.txt --output GCF_018736085.1_ASM1873608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:17,690] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:17,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:17,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:17,712] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:33:17,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:17,713] [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 sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	100.0	1850	1851	95	conclusive
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	83.4793	1278	1851	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	83.3958	1244	1851	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	83.3869	1216	1851	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	83.3326	1268	1851	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	83.1919	1249	1851	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	83.1338	1223	1851	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	83.0306	1231	1851	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.8455	1203	1851	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	82.8219	1177	1851	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	82.7547	1217	1851	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.7432	1186	1851	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.6909	1129	1851	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.5518	1128	1851	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	82.2571	1178	1851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:17,714] [INFO] DFAST Taxonomy check result was written to GCF_018736085.1_ASM1873608v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:17,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:17,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:17,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/checkm_data
[2024-01-24 14:33:17,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:17,769] [INFO] Task started: CheckM
[2024-01-24 14:33:17,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018736085.1_ASM1873608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018736085.1_ASM1873608v1_genomic.fna/checkm_input GCF_018736085.1_ASM1873608v1_genomic.fna/checkm_result
[2024-01-24 14:34:08,173] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:08,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:08,200] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:08,201] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:08,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018736085.1_ASM1873608v1_genomic.fna/markers.fasta)
[2024-01-24 14:34:08,201] [INFO] Task started: Blastn
[2024-01-24 14:34:08,202] [INFO] Running command: blastn -query GCF_018736085.1_ASM1873608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58cc061b-8a67-4f4c-9c2d-23094c31b78e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018736085.1_ASM1873608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:10,269] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:10,273] [INFO] Selected 16 target genomes.
[2024-01-24 14:34:10,273] [INFO] Target genome list was writen to GCF_018736085.1_ASM1873608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:10,287] [INFO] Task started: fastANI
[2024-01-24 14:34:10,288] [INFO] Running command: fastANI --query /var/lib/cwl/stga784ec81-51e8-4fb2-a5a2-6d9fc2a9109d/GCF_018736085.1_ASM1873608v1_genomic.fna.gz --refList GCF_018736085.1_ASM1873608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018736085.1_ASM1873608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:37,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:37,717] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:37,718] [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_018736105.1	s__Bradyrhizobium sp018736105	95.0791	1607	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.26	95.12	0.88	0.88	3	conclusive
GCA_001464035.1	s__Bradyrhizobium sp001464035	86.5008	1229	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881085.1	s__Bradyrhizobium sp017881085	84.9224	1086	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129425.1	s__Bradyrhizobium erythrophlei_C	84.7029	1199	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129675.1	s__Bradyrhizobium erythrophlei_A	84.3302	1288	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701345.1	s__Bradyrhizobium sp000701345	84.2767	1147	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141755.1	s__Bradyrhizobium lablabi_A	84.1809	1272	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099825.1	s__Bradyrhizobium ottawaense_A	84.0003	1265	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.73	99.45	0.98	0.96	3	-
GCA_004799445.1	s__Bradyrhizobium sp004799445	83.9016	1132	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103365.1	s__Bradyrhizobium sp900103365	83.7514	1249	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003062295.1	s__Bradyrhizobium algeriense	83.6468	1282	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449695.1	s__Bradyrhizobium sp018449695	83.2996	1099	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449525.1	s__Bradyrhizobium sp018449525	83.0799	1014	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398895.1	s__Bradyrhizobium sp018398895	83.0067	1251	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	82.8329	1148	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971675.1	s__Bradyrhizobium sp018971675	82.2902	706	1851	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:37,720] [INFO] GTDB search result was written to GCF_018736085.1_ASM1873608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:37,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:37,724] [INFO] DFAST_QC result json was written to GCF_018736085.1_ASM1873608v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:37,724] [INFO] DFAST_QC completed!
[2024-01-24 14:34:37,724] [INFO] Total running time: 0h2m7s