[2024-01-24 13:18:32,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,445] [INFO] DQC Reference Directory: /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference
[2024-01-24 13:18:33,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,820] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ddee78c-9305-48e4-959a-e2eafd1d6d59/GCF_000298315.2_ASM29831v2_genomic.fna.gz | prodigal -d GCF_000298315.2_ASM29831v2_genomic.fna/cds.fna -a GCF_000298315.2_ASM29831v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:56,488] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:56,489] [INFO] Task started: HMMsearch
[2024-01-24 13:18:56,489] [INFO] Running command: hmmsearch --tblout GCF_000298315.2_ASM29831v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/reference_markers.hmm GCF_000298315.2_ASM29831v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:56,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:56,896] [INFO] Found 6/6 markers.
[2024-01-24 13:18:56,956] [INFO] Query marker FASTA was written to GCF_000298315.2_ASM29831v2_genomic.fna/markers.fasta
[2024-01-24 13:18:56,956] [INFO] Task started: Blastn
[2024-01-24 13:18:56,957] [INFO] Running command: blastn -query GCF_000298315.2_ASM29831v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/reference_markers.fasta -out GCF_000298315.2_ASM29831v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:57,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:57,983] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:57,984] [INFO] Target genome list was writen to GCF_000298315.2_ASM29831v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:57,990] [INFO] Task started: fastANI
[2024-01-24 13:18:57,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ddee78c-9305-48e4-959a-e2eafd1d6d59/GCF_000298315.2_ASM29831v2_genomic.fna.gz --refList GCF_000298315.2_ASM29831v2_genomic.fna/target_genomes.txt --output GCF_000298315.2_ASM29831v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:19,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:19,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:19,498] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:19,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:19,499] [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 grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	100.0	2348	2351	95	conclusive
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	86.7845	1492	2351	95	below_threshold
Rhizobium favelukesii	strain=LPU83	GCA_000577275.2	348824	348824	type	True	85.5542	1443	2351	95	below_threshold
Rhizobium tibeticum	strain=CGMCC 1.7071	GCA_900110205.1	501024	501024	type	True	85.5279	1411	2351	95	below_threshold
Rhizobium tibeticum		GCA_900108425.1	501024	501024	type	True	85.5153	1395	2351	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.1886	949	2351	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	80.9698	985	2351	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	80.9146	1007	2351	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	79.5188	785	2351	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.3679	598	2351	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.3138	566	2351	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.2675	608	2351	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.1279	572	2351	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.8223	536	2351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,501] [INFO] DFAST Taxonomy check result was written to GCF_000298315.2_ASM29831v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:19,502] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:19,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:19,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/checkm_data
[2024-01-24 13:19:19,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:19,576] [INFO] Task started: CheckM
[2024-01-24 13:19:19,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000298315.2_ASM29831v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000298315.2_ASM29831v2_genomic.fna/checkm_input GCF_000298315.2_ASM29831v2_genomic.fna/checkm_result
[2024-01-24 13:20:20,275] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:20,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:20,298] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:20,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:20,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000298315.2_ASM29831v2_genomic.fna/markers.fasta)
[2024-01-24 13:20:20,299] [INFO] Task started: Blastn
[2024-01-24 13:20:20,299] [INFO] Running command: blastn -query GCF_000298315.2_ASM29831v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge05406ca-ba6b-49d8-898c-5ca277cff2d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000298315.2_ASM29831v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:22,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:22,173] [INFO] Selected 13 target genomes.
[2024-01-24 13:20:22,173] [INFO] Target genome list was writen to GCF_000298315.2_ASM29831v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:22,215] [INFO] Task started: fastANI
[2024-01-24 13:20:22,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ddee78c-9305-48e4-959a-e2eafd1d6d59/GCF_000298315.2_ASM29831v2_genomic.fna.gz --refList GCF_000298315.2_ASM29831v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000298315.2_ASM29831v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:41,107] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:41,129] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:41,130] [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_000298315.2	s__Rhizobium grahamii	100.0	2348	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.32	97.32	0.91	0.91	2	conclusive
GCF_014194695.1	s__Rhizobium sp014194695	92.7455	1743	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.49	98.48	0.95	0.94	4	-
GCF_001542405.1	s__Rhizobium altiplani	86.7715	1492	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.38	95.34	0.86	0.71	19	-
GCF_002211365.1	s__Rhizobium sp002211365	86.4464	1323	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.54	97.07	0.93	0.86	3	-
GCF_000282035.1	s__Rhizobium sp000282035	86.2623	1338	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.50	0.88	0.87	4	-
GCF_000312665.1	s__Rhizobium mesoamericanum	85.7701	1377	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.16	96.16	0.87	0.87	2	-
GCF_000577275.2	s__Rhizobium favelukesii	85.5533	1442	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.5244	99.59	99.23	0.94	0.89	3	-
GCF_000746265.1	s__Rhizobium sp000746265	85.3837	1322	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466605.1	s__Rhizobium sp900466605	85.2226	1315	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498215.1	s__Rhizobium grahamii_A	84.061	1084	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001429725.1	s__Rhizobium sp001429725	84.0447	1082	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900468535.1	s__Rhizobium sp900468535	83.8656	1055	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470805.1	s__Rhizobium sp900470805	81.9503	939	2351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:41,131] [INFO] GTDB search result was written to GCF_000298315.2_ASM29831v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:41,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:41,135] [INFO] DFAST_QC result json was written to GCF_000298315.2_ASM29831v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:41,136] [INFO] DFAST_QC completed!
[2024-01-24 13:20:41,136] [INFO] Total running time: 0h2m9s