[2024-01-25 20:12:05,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference
[2024-01-25 20:12:06,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,782] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ad5aede-9503-4ba5-9b26-fa01e2f55ba8/GCF_001541345.2_ASM154134v2_genomic.fna.gz | prodigal -d GCF_001541345.2_ASM154134v2_genomic.fna/cds.fna -a GCF_001541345.2_ASM154134v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:22,720] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:22,720] [INFO] Task started: HMMsearch
[2024-01-25 20:12:22,720] [INFO] Running command: hmmsearch --tblout GCF_001541345.2_ASM154134v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/reference_markers.hmm GCF_001541345.2_ASM154134v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:23,026] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:23,027] [INFO] Found 6/6 markers.
[2024-01-25 20:12:23,072] [INFO] Query marker FASTA was written to GCF_001541345.2_ASM154134v2_genomic.fna/markers.fasta
[2024-01-25 20:12:23,073] [INFO] Task started: Blastn
[2024-01-25 20:12:23,073] [INFO] Running command: blastn -query GCF_001541345.2_ASM154134v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/reference_markers.fasta -out GCF_001541345.2_ASM154134v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:23,894] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:23,897] [INFO] Selected 20 target genomes.
[2024-01-25 20:12:23,897] [INFO] Target genome list was writen to GCF_001541345.2_ASM154134v2_genomic.fna/target_genomes.txt
[2024-01-25 20:12:23,915] [INFO] Task started: fastANI
[2024-01-25 20:12:23,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad5aede-9503-4ba5-9b26-fa01e2f55ba8/GCF_001541345.2_ASM154134v2_genomic.fna.gz --refList GCF_001541345.2_ASM154134v2_genomic.fna/target_genomes.txt --output GCF_001541345.2_ASM154134v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:43,580] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:43,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:43,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:43,592] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:43,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:43,593] [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 taibaishanense	strain=DSM 100021	GCA_014196735.1	887144	887144	type	True	82.2221	1189	1908	95	below_threshold
Rhizobium taibaishanense	strain=14971	GCA_001938985.1	887144	887144	type	True	82.2208	1186	1908	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	78.9916	551	1908	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	78.6473	531	1908	95	below_threshold
Rhizobium halophytocola	strain=DSM 21600	GCA_017873095.1	735519	735519	type	True	78.6419	554	1908	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	78.5136	506	1908	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	78.4937	500	1908	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.3542	480	1908	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	78.1502	524	1908	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	78.0938	457	1908	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	78.0893	433	1908	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	78.0708	475	1908	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.0447	443	1908	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	78.0353	474	1908	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	77.9743	432	1908	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	77.9617	466	1908	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.9132	395	1908	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.8918	407	1908	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.8562	392	1908	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.7706	429	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:43,594] [INFO] DFAST Taxonomy check result was written to GCF_001541345.2_ASM154134v2_genomic.fna/tc_result.tsv
[2024-01-25 20:12:43,595] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:43,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:43,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/checkm_data
[2024-01-25 20:12:43,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:43,652] [INFO] Task started: CheckM
[2024-01-25 20:12:43,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001541345.2_ASM154134v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001541345.2_ASM154134v2_genomic.fna/checkm_input GCF_001541345.2_ASM154134v2_genomic.fna/checkm_result
[2024-01-25 20:13:30,296] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:30,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:30,314] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:30,314] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:30,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001541345.2_ASM154134v2_genomic.fna/markers.fasta)
[2024-01-25 20:13:30,315] [INFO] Task started: Blastn
[2024-01-25 20:13:30,316] [INFO] Running command: blastn -query GCF_001541345.2_ASM154134v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d321546-2585-43cd-9355-1bf87e964f5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001541345.2_ASM154134v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:31,887] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:31,889] [INFO] Selected 5 target genomes.
[2024-01-25 20:13:31,890] [INFO] Target genome list was writen to GCF_001541345.2_ASM154134v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:31,893] [INFO] Task started: fastANI
[2024-01-25 20:13:31,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad5aede-9503-4ba5-9b26-fa01e2f55ba8/GCF_001541345.2_ASM154134v2_genomic.fna.gz --refList GCF_001541345.2_ASM154134v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001541345.2_ASM154134v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:39,709] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:39,714] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:39,714] [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_001541345.2	s__Allorhizobium vitis	100.0	1904	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.04	96.12	0.92	0.85	14	conclusive
GCF_001758275.2	s__Allorhizobium vitis_B	93.9619	1656	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.87	95.34	0.94	0.85	14	-
GCF_009744025.1	s__Allorhizobium vitis_A	93.4332	1654	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.14	95.73	0.87	0.84	24	-
GCF_009744115.1	s__Allorhizobium vitis_E	93.2835	1583	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426735.1	s__Allorhizobium vitis_D	92.8542	1553	1908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.49	97.49	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:39,715] [INFO] GTDB search result was written to GCF_001541345.2_ASM154134v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:39,716] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:39,719] [INFO] DFAST_QC result json was written to GCF_001541345.2_ASM154134v2_genomic.fna/dqc_result.json
[2024-01-25 20:13:39,719] [INFO] DFAST_QC completed!
[2024-01-25 20:13:39,719] [INFO] Total running time: 0h1m34s