[2024-01-25 19:42:05,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:05,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:05,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference
[2024-01-25 19:42:06,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:06,785] [INFO] Task started: Prodigal
[2024-01-25 19:42:06,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg42ab030f-95fb-41d8-949f-dfc4ba6bec49/GCF_013378445.1_ASM1337844v1_genomic.fna.gz | prodigal -d GCF_013378445.1_ASM1337844v1_genomic.fna/cds.fna -a GCF_013378445.1_ASM1337844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:21,209] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:21,210] [INFO] Task started: HMMsearch
[2024-01-25 19:42:21,210] [INFO] Running command: hmmsearch --tblout GCF_013378445.1_ASM1337844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/reference_markers.hmm GCF_013378445.1_ASM1337844v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:21,573] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:21,574] [INFO] Found 6/6 markers.
[2024-01-25 19:42:21,639] [INFO] Query marker FASTA was written to GCF_013378445.1_ASM1337844v1_genomic.fna/markers.fasta
[2024-01-25 19:42:21,639] [INFO] Task started: Blastn
[2024-01-25 19:42:21,639] [INFO] Running command: blastn -query GCF_013378445.1_ASM1337844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/reference_markers.fasta -out GCF_013378445.1_ASM1337844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:22,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:22,677] [INFO] Selected 13 target genomes.
[2024-01-25 19:42:22,678] [INFO] Target genome list was writen to GCF_013378445.1_ASM1337844v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:22,683] [INFO] Task started: fastANI
[2024-01-25 19:42:22,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ab030f-95fb-41d8-949f-dfc4ba6bec49/GCF_013378445.1_ASM1337844v1_genomic.fna.gz --refList GCF_013378445.1_ASM1337844v1_genomic.fna/target_genomes.txt --output GCF_013378445.1_ASM1337844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:37,946] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:37,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:37,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:37,956] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:37,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:37,956] [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 rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	100.0	1839	1840	95	conclusive
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	92.3723	1528	1840	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	84.1951	1202	1840	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	82.0289	899	1840	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	81.9652	1000	1840	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	81.9283	842	1840	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	81.8714	857	1840	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	81.8662	1015	1840	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	81.7953	887	1840	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	81.3131	903	1840	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	81.311	884	1840	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	81.2233	917	1840	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	81.1097	919	1840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:37,957] [INFO] DFAST Taxonomy check result was written to GCF_013378445.1_ASM1337844v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:37,958] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:37,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:37,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/checkm_data
[2024-01-25 19:42:37,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:38,010] [INFO] Task started: CheckM
[2024-01-25 19:42:38,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013378445.1_ASM1337844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013378445.1_ASM1337844v1_genomic.fna/checkm_input GCF_013378445.1_ASM1337844v1_genomic.fna/checkm_result
[2024-01-25 19:43:19,922] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:19,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:19,945] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:19,945] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:19,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013378445.1_ASM1337844v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:19,946] [INFO] Task started: Blastn
[2024-01-25 19:43:19,946] [INFO] Running command: blastn -query GCF_013378445.1_ASM1337844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769dd84e-e5d2-4a02-b0d4-8760fd7be9ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_013378445.1_ASM1337844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:22,059] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:22,064] [INFO] Selected 8 target genomes.
[2024-01-25 19:43:22,064] [INFO] Target genome list was writen to GCF_013378445.1_ASM1337844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:22,074] [INFO] Task started: fastANI
[2024-01-25 19:43:22,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg42ab030f-95fb-41d8-949f-dfc4ba6bec49/GCF_013378445.1_ASM1337844v1_genomic.fna.gz --refList GCF_013378445.1_ASM1337844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013378445.1_ASM1337844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:32,710] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:32,716] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:32,717] [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_013378445.1	s__Mycoplana rhizolycopersici	100.0	1839	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900220975.1	s__Mycoplana subbaraonis	92.3957	1526	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	84.6363	1212	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_014196765.1	s__Mycoplana azooxidifex	84.1988	1202	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046475.1	s__Mycoplana dimorpha	82.735	957	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851675.1	s__Mycoplana sp014851675	82.1147	968	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	81.9433	840	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	81.7999	886	1840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:32,718] [INFO] GTDB search result was written to GCF_013378445.1_ASM1337844v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:32,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:32,721] [INFO] DFAST_QC result json was written to GCF_013378445.1_ASM1337844v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:32,721] [INFO] DFAST_QC completed!
[2024-01-25 19:43:32,721] [INFO] Total running time: 0h1m27s