[2024-01-24 12:44:08,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:08,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:08,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference
[2024-01-24 12:44:09,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:09,826] [INFO] Task started: Prodigal
[2024-01-24 12:44:09,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg15dc8417-299c-43ae-9722-70e14b362749/GCF_003217325.1_ASM321732v1_genomic.fna.gz | prodigal -d GCF_003217325.1_ASM321732v1_genomic.fna/cds.fna -a GCF_003217325.1_ASM321732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:21,956] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:21,957] [INFO] Task started: HMMsearch
[2024-01-24 12:44:21,957] [INFO] Running command: hmmsearch --tblout GCF_003217325.1_ASM321732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/reference_markers.hmm GCF_003217325.1_ASM321732v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:22,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:22,285] [INFO] Found 6/6 markers.
[2024-01-24 12:44:22,321] [INFO] Query marker FASTA was written to GCF_003217325.1_ASM321732v1_genomic.fna/markers.fasta
[2024-01-24 12:44:22,322] [INFO] Task started: Blastn
[2024-01-24 12:44:22,322] [INFO] Running command: blastn -query GCF_003217325.1_ASM321732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/reference_markers.fasta -out GCF_003217325.1_ASM321732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:23,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:23,366] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:23,366] [INFO] Target genome list was writen to GCF_003217325.1_ASM321732v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:23,372] [INFO] Task started: fastANI
[2024-01-24 12:44:23,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg15dc8417-299c-43ae-9722-70e14b362749/GCF_003217325.1_ASM321732v1_genomic.fna.gz --refList GCF_003217325.1_ASM321732v1_genomic.fna/target_genomes.txt --output GCF_003217325.1_ASM321732v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:40,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:40,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:40,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:40,155] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:40,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:40,155] [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
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	100.0	1323	1327	95	conclusive
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	82.6498	926	1327	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	82.0215	868	1327	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	82.0049	870	1327	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	81.7676	879	1327	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	80.564	716	1327	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	80.3885	746	1327	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	80.3844	732	1327	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	80.2303	692	1327	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	80.2134	702	1327	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	80.1031	702	1327	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	79.964	708	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:40,157] [INFO] DFAST Taxonomy check result was written to GCF_003217325.1_ASM321732v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:40,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:40,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:40,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/checkm_data
[2024-01-24 12:44:40,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:40,199] [INFO] Task started: CheckM
[2024-01-24 12:44:40,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217325.1_ASM321732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217325.1_ASM321732v1_genomic.fna/checkm_input GCF_003217325.1_ASM321732v1_genomic.fna/checkm_result
[2024-01-24 12:45:19,094] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:19,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:19,120] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:19,120] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:19,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217325.1_ASM321732v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:19,121] [INFO] Task started: Blastn
[2024-01-24 12:45:19,121] [INFO] Running command: blastn -query GCF_003217325.1_ASM321732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9843290-1b02-47d5-95c9-2baf8ac7e653/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217325.1_ASM321732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:21,189] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:21,193] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:21,193] [INFO] Target genome list was writen to GCF_003217325.1_ASM321732v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:21,207] [INFO] Task started: fastANI
[2024-01-24 12:45:21,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg15dc8417-299c-43ae-9722-70e14b362749/GCF_003217325.1_ASM321732v1_genomic.fna.gz --refList GCF_003217325.1_ASM321732v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217325.1_ASM321732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:36,681] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:36,697] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:36,697] [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_003217325.1	s__Rhodopseudomonas faecalis	100.0	1323	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.30	98.30	0.93	0.93	2	conclusive
GCF_000504425.1	s__Rhodopseudomonas palustris_C	94.8778	1147	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	95.77	95.77	0.90	0.90	2	-
GCF_000014825.1	s__Rhodopseudomonas palustris_B	83.8792	994	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203125.1	s__Rhodopseudomonas rhenobacensis	82.6598	924	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013745.1	s__Rhodopseudomonas palustris_D	82.5916	919	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215605.1	s__Rhodopseudomonas palustris_L	82.2527	872	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013365.1	s__Rhodopseudomonas palustris_J	82.1322	884	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900218015.1	s__Rhodopseudomonas pentothenatexigens	82.0123	870	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013415845.1	s__Rhodopseudomonas palustris_F	81.8355	862	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	97.90	97.49	0.94	0.92	8	-
GCF_900110435.1	s__Rhodopseudomonas pseudopalustris	81.7778	877	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.41	98.34	0.90	0.86	3	-
GCF_003226555.1	s__Rhodopseudomonas palustris_I	81.775	886	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031265.1	s__Rhodopseudomonas palustris_H	81.7066	886	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	96.56	96.03	0.93	0.93	4	-
GCF_000177255.2	s__Rhodopseudomonas palustris_G	81.6785	924	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.28	98.19	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,699] [INFO] GTDB search result was written to GCF_003217325.1_ASM321732v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:36,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:36,702] [INFO] DFAST_QC result json was written to GCF_003217325.1_ASM321732v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:36,703] [INFO] DFAST_QC completed!
[2024-01-24 12:45:36,703] [INFO] Total running time: 0h1m28s