[2024-01-24 14:55:35,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:35,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:35,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference
[2024-01-24 14:55:37,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:37,140] [INFO] Task started: Prodigal
[2024-01-24 14:55:37,140] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4c3c9f3-3ed2-4008-a0ad-55ca0ffd849a/GCF_030064585.1_ASM3006458v1_genomic.fna.gz | prodigal -d GCF_030064585.1_ASM3006458v1_genomic.fna/cds.fna -a GCF_030064585.1_ASM3006458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:56,343] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:56,343] [INFO] Task started: HMMsearch
[2024-01-24 14:55:56,343] [INFO] Running command: hmmsearch --tblout GCF_030064585.1_ASM3006458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/reference_markers.hmm GCF_030064585.1_ASM3006458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:56,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:56,700] [INFO] Found 6/6 markers.
[2024-01-24 14:55:56,763] [INFO] Query marker FASTA was written to GCF_030064585.1_ASM3006458v1_genomic.fna/markers.fasta
[2024-01-24 14:55:56,763] [INFO] Task started: Blastn
[2024-01-24 14:55:56,763] [INFO] Running command: blastn -query GCF_030064585.1_ASM3006458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/reference_markers.fasta -out GCF_030064585.1_ASM3006458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:57,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:57,858] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:57,858] [INFO] Target genome list was writen to GCF_030064585.1_ASM3006458v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:57,864] [INFO] Task started: fastANI
[2024-01-24 14:55:57,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4c3c9f3-3ed2-4008-a0ad-55ca0ffd849a/GCF_030064585.1_ASM3006458v1_genomic.fna.gz --refList GCF_030064585.1_ASM3006458v1_genomic.fna/target_genomes.txt --output GCF_030064585.1_ASM3006458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:15,199] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:15,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:15,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:15,213] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:15,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:15,214] [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
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	98.3612	1814	2197	95	conclusive
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	98.3445	1982	2197	95	conclusive
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	98.2859	1906	2197	95	conclusive
Sinorhizobium arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	90.3964	1648	2197	95	below_threshold
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	87.3051	1693	2197	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	82.3034	1067	2197	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.72	766	2197	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.3482	756	2197	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.3341	934	2197	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.9085	730	2197	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.2421	609	2197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,216] [INFO] DFAST Taxonomy check result was written to GCF_030064585.1_ASM3006458v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:15,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:15,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:15,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/checkm_data
[2024-01-24 14:56:15,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,398] [INFO] Task started: CheckM
[2024-01-24 14:56:15,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030064585.1_ASM3006458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030064585.1_ASM3006458v1_genomic.fna/checkm_input GCF_030064585.1_ASM3006458v1_genomic.fna/checkm_result
[2024-01-24 14:57:11,175] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:11,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:11,202] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:11,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:11,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030064585.1_ASM3006458v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:11,203] [INFO] Task started: Blastn
[2024-01-24 14:57:11,203] [INFO] Running command: blastn -query GCF_030064585.1_ASM3006458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef5c3c1-c571-4457-81fb-9073ca8d2426/dqc_reference/reference_markers_gtdb.fasta -out GCF_030064585.1_ASM3006458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:13,328] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:13,336] [INFO] Selected 6 target genomes.
[2024-01-24 14:57:13,336] [INFO] Target genome list was writen to GCF_030064585.1_ASM3006458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:13,342] [INFO] Task started: fastANI
[2024-01-24 14:57:13,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4c3c9f3-3ed2-4008-a0ad-55ca0ffd849a/GCF_030064585.1_ASM3006458v1_genomic.fna.gz --refList GCF_030064585.1_ASM3006458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030064585.1_ASM3006458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:25,748] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:25,759] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:25,759] [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_017876815.1	s__Sinorhizobium meliloti	98.3445	1982	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.94	97.48	0.91	0.82	239	conclusive
GCA_000421085.1	s__Sinorhizobium sp000421085	94.3503	1752	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375585.1	s__Sinorhizobium meliloti_A	94.0127	1697	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	97.48	0.86	0.81	5	-
GCF_000427465.1	s__Sinorhizobium arboris	90.3991	1648	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827695.1	s__Sinorhizobium medicae	87.2955	1675	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.40	99.02	0.92	0.89	63	-
GCF_001651875.1	s__Sinorhizobium saheli	84.1814	1245	2197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:25,761] [INFO] GTDB search result was written to GCF_030064585.1_ASM3006458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:25,761] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:25,764] [INFO] DFAST_QC result json was written to GCF_030064585.1_ASM3006458v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:25,764] [INFO] DFAST_QC completed!
[2024-01-24 14:57:25,765] [INFO] Total running time: 0h1m50s