[2024-01-24 15:02:33,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference
[2024-01-24 15:02:34,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,868] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg00f62dff-9d09-4451-987b-17e6e2dcfdbe/GCF_001440475.1_ASM144047v1_genomic.fna.gz | prodigal -d GCF_001440475.1_ASM144047v1_genomic.fna/cds.fna -a GCF_001440475.1_ASM144047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:01,165] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:01,166] [INFO] Task started: HMMsearch
[2024-01-24 15:03:01,166] [INFO] Running command: hmmsearch --tblout GCF_001440475.1_ASM144047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/reference_markers.hmm GCF_001440475.1_ASM144047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:01,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:01,635] [INFO] Found 6/6 markers.
[2024-01-24 15:03:01,700] [INFO] Query marker FASTA was written to GCF_001440475.1_ASM144047v1_genomic.fna/markers.fasta
[2024-01-24 15:03:01,700] [INFO] Task started: Blastn
[2024-01-24 15:03:01,701] [INFO] Running command: blastn -query GCF_001440475.1_ASM144047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/reference_markers.fasta -out GCF_001440475.1_ASM144047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:02,778] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:02,781] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:02,781] [INFO] Target genome list was writen to GCF_001440475.1_ASM144047v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:02,786] [INFO] Task started: fastANI
[2024-01-24 15:03:02,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg00f62dff-9d09-4451-987b-17e6e2dcfdbe/GCF_001440475.1_ASM144047v1_genomic.fna.gz --refList GCF_001440475.1_ASM144047v1_genomic.fna/target_genomes.txt --output GCF_001440475.1_ASM144047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:36,287] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:36,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:36,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:36,301] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:36,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:36,302] [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 lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	100.0	2861	2871	95	conclusive
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	92.7632	2247	2871	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	91.8195	2160	2871	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	87.9894	1956	2871	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	87.9659	1878	2871	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	87.9177	1955	2871	95	below_threshold
Bradyrhizobium archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	87.747	1846	2871	95	below_threshold
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	87.714	1864	2871	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	87.6959	1931	2871	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	83.1015	1562	2871	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	83.0763	1583	2871	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9385	1506	2871	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.9266	1424	2871	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8459	1438	2871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:36,304] [INFO] DFAST Taxonomy check result was written to GCF_001440475.1_ASM144047v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:36,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:36,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:36,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/checkm_data
[2024-01-24 15:03:36,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:36,399] [INFO] Task started: CheckM
[2024-01-24 15:03:36,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001440475.1_ASM144047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001440475.1_ASM144047v1_genomic.fna/checkm_input GCF_001440475.1_ASM144047v1_genomic.fna/checkm_result
[2024-01-24 15:04:50,066] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:50,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:50,098] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:50,099] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:50,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001440475.1_ASM144047v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:50,100] [INFO] Task started: Blastn
[2024-01-24 15:04:50,100] [INFO] Running command: blastn -query GCF_001440475.1_ASM144047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2590c9e8-ce00-47f2-adfc-13d3fd37b8fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001440475.1_ASM144047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:52,214] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:52,218] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:52,218] [INFO] Target genome list was writen to GCF_001440475.1_ASM144047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:52,228] [INFO] Task started: fastANI
[2024-01-24 15:04:52,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg00f62dff-9d09-4451-987b-17e6e2dcfdbe/GCF_001440475.1_ASM144047v1_genomic.fna.gz --refList GCF_001440475.1_ASM144047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001440475.1_ASM144047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:23,107] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:23,120] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:23,121] [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_001440475.1	s__Bradyrhizobium lablabi	100.0	2861	2871	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_001693515.2	s__Bradyrhizobium paxllaeri	92.7662	2246	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440395.1	s__Bradyrhizobium jicamae	91.8191	2160	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009930815.1	s__Bradyrhizobium sp009930815	91.5747	2253	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596315.1	s__Bradyrhizobium sp018596315	88.1701	2140	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693485.1	s__Bradyrhizobium sp001693485	88.0889	1986	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472965.1	s__Bradyrhizobium murdochi	87.9726	1960	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693385.1	s__Bradyrhizobium icense	87.9372	1952	2871	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	87.9066	2054	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440405.1	s__Bradyrhizobium valentinum	87.7334	1924	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	99.35	0.91	0.91	2	-
GCF_018398895.1	s__Bradyrhizobium sp018398895	87.6354	1934	2871	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398875.1	s__Bradyrhizobium sp018398875	87.6038	1874	2871	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 15:05:23,123] [INFO] GTDB search result was written to GCF_001440475.1_ASM144047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:23,124] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:23,131] [INFO] DFAST_QC result json was written to GCF_001440475.1_ASM144047v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:23,132] [INFO] DFAST_QC completed!
[2024-01-24 15:05:23,132] [INFO] Total running time: 0h2m50s