[2024-01-25 18:44:50,783] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:50,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:50,785] [INFO] DQC Reference Directory: /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference
[2024-01-25 18:44:51,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:51,887] [INFO] Task started: Prodigal
[2024-01-25 18:44:51,887] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc2acb83-145c-45d3-a986-fcdab054c2ef/GCF_030036535.1_ASM3003653v1_genomic.fna.gz | prodigal -d GCF_030036535.1_ASM3003653v1_genomic.fna/cds.fna -a GCF_030036535.1_ASM3003653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:07,544] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:07,545] [INFO] Task started: HMMsearch
[2024-01-25 18:45:07,545] [INFO] Running command: hmmsearch --tblout GCF_030036535.1_ASM3003653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/reference_markers.hmm GCF_030036535.1_ASM3003653v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:07,984] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:07,985] [INFO] Found 6/6 markers.
[2024-01-25 18:45:08,036] [INFO] Query marker FASTA was written to GCF_030036535.1_ASM3003653v1_genomic.fna/markers.fasta
[2024-01-25 18:45:08,037] [INFO] Task started: Blastn
[2024-01-25 18:45:08,037] [INFO] Running command: blastn -query GCF_030036535.1_ASM3003653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/reference_markers.fasta -out GCF_030036535.1_ASM3003653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:08,959] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:08,962] [INFO] Selected 11 target genomes.
[2024-01-25 18:45:08,962] [INFO] Target genome list was writen to GCF_030036535.1_ASM3003653v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:08,971] [INFO] Task started: fastANI
[2024-01-25 18:45:08,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2acb83-145c-45d3-a986-fcdab054c2ef/GCF_030036535.1_ASM3003653v1_genomic.fna.gz --refList GCF_030036535.1_ASM3003653v1_genomic.fna/target_genomes.txt --output GCF_030036535.1_ASM3003653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:22,258] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:22,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:22,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:22,266] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:22,266] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:22,266] [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
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	89.5685	1404	1898	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	88.9216	1439	1898	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	88.9165	1422	1898	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	88.8945	1432	1898	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	88.8223	1424	1898	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	88.3423	1356	1898	95	below_threshold
Rhizobium pusense	strain=NRCPB10	GCA_002008275.1	648995	648995	type	True	87.262	1361	1898	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	87.2238	1371	1898	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	79.8165	700	1898	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	79.798	702	1898	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5673	601	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:22,268] [INFO] DFAST Taxonomy check result was written to GCF_030036535.1_ASM3003653v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:22,268] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:22,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:22,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/checkm_data
[2024-01-25 18:45:22,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:22,323] [INFO] Task started: CheckM
[2024-01-25 18:45:22,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030036535.1_ASM3003653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030036535.1_ASM3003653v1_genomic.fna/checkm_input GCF_030036535.1_ASM3003653v1_genomic.fna/checkm_result
[2024-01-25 18:46:08,241] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:08,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:08,262] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:08,263] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:08,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030036535.1_ASM3003653v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:08,264] [INFO] Task started: Blastn
[2024-01-25 18:46:08,264] [INFO] Running command: blastn -query GCF_030036535.1_ASM3003653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6b00628-cda6-4f79-9580-8af4ef4cd5ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_030036535.1_ASM3003653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:10,145] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:10,148] [INFO] Selected 11 target genomes.
[2024-01-25 18:46:10,148] [INFO] Target genome list was writen to GCF_030036535.1_ASM3003653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:10,168] [INFO] Task started: fastANI
[2024-01-25 18:46:10,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2acb83-145c-45d3-a986-fcdab054c2ef/GCF_030036535.1_ASM3003653v1_genomic.fna.gz --refList GCF_030036535.1_ASM3003653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030036535.1_ASM3003653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:24,985] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:24,993] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:24,993] [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_007002745.1	s__Agrobacterium rhizogenes_B	98.1944	1766	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005221385.1	s__Agrobacterium sp900013535	93.7974	1551	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.00	98.18	0.90	0.86	7	-
GCF_013337285.1	s__Agrobacterium tumefaciens_H	92.8994	1478	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	97.88	0.96	0.94	4	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	92.6947	1551	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_900012615.1	s__Agrobacterium sp900012615	89.3779	1426	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCF_002943835.1	s__Agrobacterium deltaense	89.293	1423	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	88.908	1377	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001541315.1	s__Agrobacterium tumefaciens	88.9006	1431	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	88.831	1426	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCA_003241215.1	s__Agrobacterium fabrum_A	88.5202	1001	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	88.0302	1377	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:24,994] [INFO] GTDB search result was written to GCF_030036535.1_ASM3003653v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:24,995] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:24,997] [INFO] DFAST_QC result json was written to GCF_030036535.1_ASM3003653v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:24,997] [INFO] DFAST_QC completed!
[2024-01-25 18:46:24,997] [INFO] Total running time: 0h1m34s