[2024-01-25 18:46:35,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference
[2024-01-25 18:46:36,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,798] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,798] [INFO] Running command: gunzip -c /var/lib/cwl/stgd35de922-b11e-4cfa-9067-e9363a274f1f/GCF_003240585.1_ASM324058v1_genomic.fna.gz | prodigal -d GCF_003240585.1_ASM324058v1_genomic.fna/cds.fna -a GCF_003240585.1_ASM324058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:53,875] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:53,875] [INFO] Task started: HMMsearch
[2024-01-25 18:46:53,875] [INFO] Running command: hmmsearch --tblout GCF_003240585.1_ASM324058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/reference_markers.hmm GCF_003240585.1_ASM324058v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:54,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:54,288] [INFO] Found 6/6 markers.
[2024-01-25 18:46:54,340] [INFO] Query marker FASTA was written to GCF_003240585.1_ASM324058v1_genomic.fna/markers.fasta
[2024-01-25 18:46:54,340] [INFO] Task started: Blastn
[2024-01-25 18:46:54,340] [INFO] Running command: blastn -query GCF_003240585.1_ASM324058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/reference_markers.fasta -out GCF_003240585.1_ASM324058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:55,186] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:55,189] [INFO] Selected 26 target genomes.
[2024-01-25 18:46:55,189] [INFO] Target genome list was writen to GCF_003240585.1_ASM324058v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:55,248] [INFO] Task started: fastANI
[2024-01-25 18:46:55,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgd35de922-b11e-4cfa-9067-e9363a274f1f/GCF_003240585.1_ASM324058v1_genomic.fna.gz --refList GCF_003240585.1_ASM324058v1_genomic.fna/target_genomes.txt --output GCF_003240585.1_ASM324058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:27,869] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:27,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:27,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:27,884] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:27,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:27,884] [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 tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	100.0	2140	2146	95	conclusive
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	80.447	956	2146	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	80.4441	954	2146	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	80.0951	953	2146	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	80.0598	978	2146	95	below_threshold
Rhizobium metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	80.0566	775	2146	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.0125	862	2146	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	80.012	869	2146	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	80.0076	865	2146	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	79.9917	872	2146	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	79.9838	866	2146	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	79.9722	880	2146	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.97	840	2146	95	below_threshold
Rhizobium tumorigenes	strain=1078	GCA_003240565.1	2041385	2041385	type	True	79.9586	861	2146	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	79.8981	893	2146	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	79.8681	834	2146	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	79.61	826	2146	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	79.5692	814	2146	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	79.2782	842	2146	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	79.254	767	2146	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	79.1969	582	2146	95	below_threshold
Rhizobium mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	79.1235	773	2146	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.1119	591	2146	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.0461	750	2146	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.88	617	2146	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.7521	599	2146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:27,887] [INFO] DFAST Taxonomy check result was written to GCF_003240585.1_ASM324058v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:27,888] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:27,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:27,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/checkm_data
[2024-01-25 18:47:27,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:27,951] [INFO] Task started: CheckM
[2024-01-25 18:47:27,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003240585.1_ASM324058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003240585.1_ASM324058v1_genomic.fna/checkm_input GCF_003240585.1_ASM324058v1_genomic.fna/checkm_result
[2024-01-25 18:48:16,164] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:16,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:16,180] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:16,181] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:16,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003240585.1_ASM324058v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:16,182] [INFO] Task started: Blastn
[2024-01-25 18:48:16,182] [INFO] Running command: blastn -query GCF_003240585.1_ASM324058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c4cce59-85cd-42d5-9b33-fcb697a431cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003240585.1_ASM324058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:17,871] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:17,873] [INFO] Selected 23 target genomes.
[2024-01-25 18:48:17,873] [INFO] Target genome list was writen to GCF_003240585.1_ASM324058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:17,898] [INFO] Task started: fastANI
[2024-01-25 18:48:17,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgd35de922-b11e-4cfa-9067-e9363a274f1f/GCF_003240585.1_ASM324058v1_genomic.fna.gz --refList GCF_003240585.1_ASM324058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003240585.1_ASM324058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:50,318] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:50,331] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:50,331] [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_003240585.1	s__Rhizobium tubonense	100.0	2140	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014195095.1	s__Rhizobium sp014195095	80.673	967	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498525.1	s__Rhizobium sp009498525	80.4832	951	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864575.1	s__Rhizobium sp900468685	80.2794	828	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.95	0.90	0.89	5	-
GCF_007000325.1	s__Rhizobium sp007000325	80.1782	827	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.07	97.10	0.92	0.88	7	-
GCF_004341625.1	s__Rhizobium sp004341625	80.167	1008	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	80.1644	875	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_000172795.2	s__Rhizobium sp000172795	80.1242	867	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211285.1	s__Rhizobium sp002211285	80.1172	836	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706285.1	s__Rhizobium sp902706285	80.0702	776	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627755.1	s__Rhizobium jaguaris	80.0516	980	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094555.1	s__Rhizobium hainanense	79.9995	871	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003240565.1	s__Rhizobium tumorigenes	79.9526	862	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.15	97.15	0.93	0.93	2	-
GCA_900472625.1	s__Rhizobium sp900472625	79.9501	776	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001657485.1	s__Rhizobium sp001657485	79.9344	895	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCA_900470805.1	s__Rhizobium sp900470805	79.7865	763	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197535.1	s__Rhizobium aethiopicum_A	79.782	831	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	79.7721	878	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472605.1	s__Rhizobium sp900472605	79.7181	760	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.47	95.34	0.81	0.80	4	-
GCF_004345245.1	s__Rhizobium sp004345245	79.4122	807	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900468805.1	s__Rhizobium sp900468805	79.3753	828	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.10	98.22	0.94	0.90	7	-
GCF_009498215.1	s__Rhizobium grahamii_A	79.365	692	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900466475.1	s__Rhizobium sp900466475	79.2349	817	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.15	97.80	0.95	0.94	17	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:50,334] [INFO] GTDB search result was written to GCF_003240585.1_ASM324058v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:50,334] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:50,339] [INFO] DFAST_QC result json was written to GCF_003240585.1_ASM324058v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:50,339] [INFO] DFAST_QC completed!
[2024-01-25 18:48:50,339] [INFO] Total running time: 0h2m15s