[2024-01-24 13:17:34,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference
[2024-01-24 13:17:35,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,517] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a974d60-49fe-4d1d-b563-5b38e46cd066/GCF_006443685.1_ASM644368v1_genomic.fna.gz | prodigal -d GCF_006443685.1_ASM644368v1_genomic.fna/cds.fna -a GCF_006443685.1_ASM644368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:50,159] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:50,159] [INFO] Task started: HMMsearch
[2024-01-24 13:17:50,160] [INFO] Running command: hmmsearch --tblout GCF_006443685.1_ASM644368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/reference_markers.hmm GCF_006443685.1_ASM644368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:50,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:50,451] [INFO] Found 6/6 markers.
[2024-01-24 13:17:50,498] [INFO] Query marker FASTA was written to GCF_006443685.1_ASM644368v1_genomic.fna/markers.fasta
[2024-01-24 13:17:50,499] [INFO] Task started: Blastn
[2024-01-24 13:17:50,501] [INFO] Running command: blastn -query GCF_006443685.1_ASM644368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/reference_markers.fasta -out GCF_006443685.1_ASM644368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:51,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:51,524] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:51,525] [INFO] Target genome list was writen to GCF_006443685.1_ASM644368v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:51,529] [INFO] Task started: fastANI
[2024-01-24 13:17:51,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a974d60-49fe-4d1d-b563-5b38e46cd066/GCF_006443685.1_ASM644368v1_genomic.fna.gz --refList GCF_006443685.1_ASM644368v1_genomic.fna/target_genomes.txt --output GCF_006443685.1_ASM644368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:02,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:02,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,349] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:02,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:02,350] [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
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	100.0	1606	1607	95	conclusive
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	85.7261	1210	1607	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	84.0437	1051	1607	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	83.9146	1066	1607	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	83.4435	1071	1607	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	80.3344	661	1607	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	79.1514	566	1607	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.0037	490	1607	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	78.2839	375	1607	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.2767	380	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,351] [INFO] DFAST Taxonomy check result was written to GCF_006443685.1_ASM644368v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,352] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/checkm_data
[2024-01-24 13:18:02,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,407] [INFO] Task started: CheckM
[2024-01-24 13:18:02,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006443685.1_ASM644368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006443685.1_ASM644368v1_genomic.fna/checkm_input GCF_006443685.1_ASM644368v1_genomic.fna/checkm_result
[2024-01-24 13:18:47,878] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:47,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:47,908] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:47,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:47,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006443685.1_ASM644368v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:47,909] [INFO] Task started: Blastn
[2024-01-24 13:18:47,909] [INFO] Running command: blastn -query GCF_006443685.1_ASM644368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg180202d6-ba99-4e25-b4db-14093cb86371/dqc_reference/reference_markers_gtdb.fasta -out GCF_006443685.1_ASM644368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,152] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:50,152] [INFO] Target genome list was writen to GCF_006443685.1_ASM644368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:50,167] [INFO] Task started: fastANI
[2024-01-24 13:18:50,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a974d60-49fe-4d1d-b563-5b38e46cd066/GCF_006443685.1_ASM644368v1_genomic.fna.gz --refList GCF_006443685.1_ASM644368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006443685.1_ASM644368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:03,190] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:03,203] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:03,203] [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_006443685.1	s__Allorhizobium glycinendophyticum	100.0	1606	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001429245.1	s__Allorhizobium sp001429245	90.5217	1288	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900473805.1	s__Allorhizobium sp900473805	86.2931	1196	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_003205195.1	s__Allorhizobium wuzhouense	85.7332	1208	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCF_014237835.1	s__Allorhizobium sp014237835	83.9794	1016	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	83.8914	1067	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_002855515.1	s__Allorhizobium sp002855515	83.7738	1071	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713475.1	s__Allorhizobium sp001713475	83.5947	1005	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCF_004912145.1	s__Allorhizobium rhizophilum	83.4454	1072	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
GCA_900466945.1	s__Allorhizobium sp900466945	83.4437	1053	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016806065.1	s__Allorhizobium sp001724035	83.4092	1042	1607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,205] [INFO] GTDB search result was written to GCF_006443685.1_ASM644368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:03,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:03,209] [INFO] DFAST_QC result json was written to GCF_006443685.1_ASM644368v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:03,209] [INFO] DFAST_QC completed!
[2024-01-24 13:19:03,209] [INFO] Total running time: 0h1m29s