[2024-01-24 15:10:54,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference
[2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,634] [INFO] Running command: gunzip -c /var/lib/cwl/stga777530b-c1a3-4a57-bec2-2248840eb508/GCF_015704895.1_ASM1570489v1_genomic.fna.gz | prodigal -d GCF_015704895.1_ASM1570489v1_genomic.fna/cds.fna -a GCF_015704895.1_ASM1570489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:13,641] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:13,641] [INFO] Task started: HMMsearch
[2024-01-24 15:11:13,642] [INFO] Running command: hmmsearch --tblout GCF_015704895.1_ASM1570489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/reference_markers.hmm GCF_015704895.1_ASM1570489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:13,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:13,979] [INFO] Found 6/6 markers.
[2024-01-24 15:11:14,032] [INFO] Query marker FASTA was written to GCF_015704895.1_ASM1570489v1_genomic.fna/markers.fasta
[2024-01-24 15:11:14,033] [INFO] Task started: Blastn
[2024-01-24 15:11:14,033] [INFO] Running command: blastn -query GCF_015704895.1_ASM1570489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/reference_markers.fasta -out GCF_015704895.1_ASM1570489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:15,035] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:15,048] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:15,049] [INFO] Target genome list was writen to GCF_015704895.1_ASM1570489v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:15,054] [INFO] Task started: fastANI
[2024-01-24 15:11:15,054] [INFO] Running command: fastANI --query /var/lib/cwl/stga777530b-c1a3-4a57-bec2-2248840eb508/GCF_015704895.1_ASM1570489v1_genomic.fna.gz --refList GCF_015704895.1_ASM1570489v1_genomic.fna/target_genomes.txt --output GCF_015704895.1_ASM1570489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:28,778] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:28,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:28,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:28,793] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:28,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:28,794] [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	100.0	1792	1798	95	conclusive
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	92.7683	1379	1798	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	92.0881	1499	1798	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	92.0299	1488	1798	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	92.0207	1492	1798	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	89.4294	1380	1798	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	89.0839	1361	1798	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.7952	625	1798	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.3455	631	1798	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.3372	741	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:28,796] [INFO] DFAST Taxonomy check result was written to GCF_015704895.1_ASM1570489v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:28,797] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:28,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:28,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/checkm_data
[2024-01-24 15:11:28,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:28,851] [INFO] Task started: CheckM
[2024-01-24 15:11:28,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015704895.1_ASM1570489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015704895.1_ASM1570489v1_genomic.fna/checkm_input GCF_015704895.1_ASM1570489v1_genomic.fna/checkm_result
[2024-01-24 15:12:18,027] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:18,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:18,048] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:18,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:18,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015704895.1_ASM1570489v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:18,050] [INFO] Task started: Blastn
[2024-01-24 15:12:18,050] [INFO] Running command: blastn -query GCF_015704895.1_ASM1570489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73df063f-dafb-47f6-b72e-a9de5126225b/dqc_reference/reference_markers_gtdb.fasta -out GCF_015704895.1_ASM1570489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:20,033] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:20,038] [INFO] Selected 9 target genomes.
[2024-01-24 15:12:20,038] [INFO] Target genome list was writen to GCF_015704895.1_ASM1570489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:20,045] [INFO] Task started: fastANI
[2024-01-24 15:12:20,046] [INFO] Running command: fastANI --query /var/lib/cwl/stga777530b-c1a3-4a57-bec2-2248840eb508/GCF_015704895.1_ASM1570489v1_genomic.fna.gz --refList GCF_015704895.1_ASM1570489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015704895.1_ASM1570489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:32,889] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:32,902] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:32,903] [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_002943835.1	s__Agrobacterium deltaense	95.8286	1500	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	conclusive
GCF_002008225.1	s__Agrobacterium salinitolerans	92.7683	1379	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCA_003241215.1	s__Agrobacterium fabrum_A	92.2039	1037	1798	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	92.0207	1492	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCF_900012615.1	s__Agrobacterium sp900012615	91.0065	1421	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	90.6405	1444	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	90.3987	1411	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	89.4509	1378	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCF_900102105.1	s__Agrobacterium pusense	89.0839	1361	1798	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.39	97.95	0.91	0.74	79	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:32,904] [INFO] GTDB search result was written to GCF_015704895.1_ASM1570489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:32,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:32,907] [INFO] DFAST_QC result json was written to GCF_015704895.1_ASM1570489v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:32,908] [INFO] DFAST_QC completed!
[2024-01-24 15:12:32,908] [INFO] Total running time: 0h1m39s