[2024-01-25 19:54:50,686] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:50,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:50,687] [INFO] DQC Reference Directory: /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference
[2024-01-25 19:54:51,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:51,850] [INFO] Task started: Prodigal
[2024-01-25 19:54:51,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg403b32fe-5d71-4f09-84a5-c980c30d9ff5/GCF_007000325.2_ASM700032v2_genomic.fna.gz | prodigal -d GCF_007000325.2_ASM700032v2_genomic.fna/cds.fna -a GCF_007000325.2_ASM700032v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:08,093] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:08,093] [INFO] Task started: HMMsearch
[2024-01-25 19:55:08,093] [INFO] Running command: hmmsearch --tblout GCF_007000325.2_ASM700032v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/reference_markers.hmm GCF_007000325.2_ASM700032v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:08,509] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:08,510] [INFO] Found 6/6 markers.
[2024-01-25 19:55:08,573] [INFO] Query marker FASTA was written to GCF_007000325.2_ASM700032v2_genomic.fna/markers.fasta
[2024-01-25 19:55:08,574] [INFO] Task started: Blastn
[2024-01-25 19:55:08,574] [INFO] Running command: blastn -query GCF_007000325.2_ASM700032v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/reference_markers.fasta -out GCF_007000325.2_ASM700032v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:09,547] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:09,550] [INFO] Selected 28 target genomes.
[2024-01-25 19:55:09,550] [INFO] Target genome list was writen to GCF_007000325.2_ASM700032v2_genomic.fna/target_genomes.txt
[2024-01-25 19:55:09,560] [INFO] Task started: fastANI
[2024-01-25 19:55:09,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg403b32fe-5d71-4f09-84a5-c980c30d9ff5/GCF_007000325.2_ASM700032v2_genomic.fna.gz --refList GCF_007000325.2_ASM700032v2_genomic.fna/target_genomes.txt --output GCF_007000325.2_ASM700032v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:44,621] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:44,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:44,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:44,638] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:55:44,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:55:44,639] [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 tumorigenes	strain=1078	GCA_003240565.1	2041385	2041385	type	True	93.7928	1565	1985	95	below_threshold
Rhizobium tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	80.1156	870	1985	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	80.0701	855	1985	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	79.9444	875	1985	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	79.8269	773	1985	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.7671	781	1985	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	79.6014	805	1985	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	79.5868	749	1985	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	79.5752	818	1985	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	79.5589	816	1985	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	79.5568	759	1985	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	79.538	772	1985	95	below_threshold
Rhizobium leucaenae	strain=CFN 299	GCA_014727215.1	29450	29450	type	True	79.5166	749	1985	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	79.5041	811	1985	95	below_threshold
Rhizobium leucaenae	strain=USDA 9039	GCA_000426285.1	29450	29450	type	True	79.4997	756	1985	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	79.4845	809	1985	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	79.4431	803	1985	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	79.3601	753	1985	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.0123	571	1985	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	78.9922	564	1985	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.9522	619	1985	95	below_threshold
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	78.894	619	1985	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	78.8821	603	1985	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.8717	569	1985	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.8662	651	1985	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	78.7809	579	1985	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	78.7595	578	1985	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4825	513	1985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:44,640] [INFO] DFAST Taxonomy check result was written to GCF_007000325.2_ASM700032v2_genomic.fna/tc_result.tsv
[2024-01-25 19:55:44,640] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:44,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:44,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/checkm_data
[2024-01-25 19:55:44,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:44,700] [INFO] Task started: CheckM
[2024-01-25 19:55:44,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007000325.2_ASM700032v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007000325.2_ASM700032v2_genomic.fna/checkm_input GCF_007000325.2_ASM700032v2_genomic.fna/checkm_result
[2024-01-25 19:56:30,127] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:30,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:30,145] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:30,145] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:30,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007000325.2_ASM700032v2_genomic.fna/markers.fasta)
[2024-01-25 19:56:30,146] [INFO] Task started: Blastn
[2024-01-25 19:56:30,147] [INFO] Running command: blastn -query GCF_007000325.2_ASM700032v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge0a59d57-30a1-4ae7-8493-d658fb48cea6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007000325.2_ASM700032v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:32,029] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:32,032] [INFO] Selected 22 target genomes.
[2024-01-25 19:56:32,032] [INFO] Target genome list was writen to GCF_007000325.2_ASM700032v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:32,052] [INFO] Task started: fastANI
[2024-01-25 19:56:32,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg403b32fe-5d71-4f09-84a5-c980c30d9ff5/GCF_007000325.2_ASM700032v2_genomic.fna.gz --refList GCF_007000325.2_ASM700032v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007000325.2_ASM700032v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:00,803] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:00,816] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:00,816] [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_007000325.1	s__Rhizobium sp007000325	99.9719	1894	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.07	97.10	0.92	0.88	7	conclusive
GCF_003240565.1	s__Rhizobium tumorigenes	93.7803	1566	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.15	97.15	0.93	0.93	2	-
GCF_003240585.1	s__Rhizobium tubonense	80.1274	869	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	80.1141	885	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189535.1	s__Rhizobium lusitanum_C	79.8904	856	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341625.1	s__Rhizobium sp004341625	79.8815	823	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.83	97.83	0.87	0.87	2	-
GCF_002211285.1	s__Rhizobium sp002211285	79.8643	750	1985	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	79.8188	755	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531755.2	s__Rhizobium acidisoli	79.768	818	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_002531935.1	s__Rhizobium chutanense	79.755	783	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.76	96.76	0.89	0.89	2	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	79.7485	821	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCA_900471515.1	s__Rhizobium sp900471515	79.6508	737	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCA_900465675.1	s__Rhizobium sp900465675	79.6112	759	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	96.80	0.93	0.89	7	-
GCF_900094555.1	s__Rhizobium hainanense	79.5069	810	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471925.1	s__Rhizobium sp900471925	79.1905	729	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466475.1	s__Rhizobium sp900466475	79.1335	721	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.15	97.80	0.95	0.94	17	-
GCF_017873135.1	s__Pararhizobium herbae	79.1042	669	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744505.1	s__Rhizobium alamii	79.0616	736	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.05	95.76	0.86	0.84	29	-
GCA_900473795.1	s__Pararhizobium sp900473795	79.0605	606	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.56	99.35	0.89	0.88	3	-
GCF_001424945.1	s__Rhizobium sp001424945	79.0257	635	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.84	96.05	0.91	0.86	3	-
GCF_000379605.1	s__Pararhizobium giardinii	78.9941	597	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	98.65	96.17	0.91	0.82	6	-
GCA_900466605.1	s__Rhizobium sp900466605	78.8516	565	1985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:00,818] [INFO] GTDB search result was written to GCF_007000325.2_ASM700032v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:00,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:00,822] [INFO] DFAST_QC result json was written to GCF_007000325.2_ASM700032v2_genomic.fna/dqc_result.json
[2024-01-25 19:57:00,822] [INFO] DFAST_QC completed!
[2024-01-25 19:57:00,822] [INFO] Total running time: 0h2m10s