[2024-01-24 14:39:34,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference
[2024-01-24 14:39:36,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,895] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg639c1fff-8e60-4f5e-af0b-34adddbc08d6/GCF_010669145.1_ASM1066914v1_genomic.fna.gz | prodigal -d GCF_010669145.1_ASM1066914v1_genomic.fna/cds.fna -a GCF_010669145.1_ASM1066914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:56,496] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:56,496] [INFO] Task started: HMMsearch
[2024-01-24 14:39:56,496] [INFO] Running command: hmmsearch --tblout GCF_010669145.1_ASM1066914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/reference_markers.hmm GCF_010669145.1_ASM1066914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:56,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:56,866] [INFO] Found 6/6 markers.
[2024-01-24 14:39:56,925] [INFO] Query marker FASTA was written to GCF_010669145.1_ASM1066914v1_genomic.fna/markers.fasta
[2024-01-24 14:39:56,925] [INFO] Task started: Blastn
[2024-01-24 14:39:56,926] [INFO] Running command: blastn -query GCF_010669145.1_ASM1066914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/reference_markers.fasta -out GCF_010669145.1_ASM1066914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:58,012] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:58,055] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:58,056] [INFO] Target genome list was writen to GCF_010669145.1_ASM1066914v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:58,109] [INFO] Task started: fastANI
[2024-01-24 14:39:58,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg639c1fff-8e60-4f5e-af0b-34adddbc08d6/GCF_010669145.1_ASM1066914v1_genomic.fna.gz --refList GCF_010669145.1_ASM1066914v1_genomic.fna/target_genomes.txt --output GCF_010669145.1_ASM1066914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:12,775] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:12,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:12,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:12,790] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:12,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:12,791] [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 oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	100.0	1939	1949	95	conclusive
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	89.4421	1381	1949	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	88.9272	1413	1949	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	88.9152	1394	1949	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	88.8551	1409	1949	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	88.0843	1295	1949	95	below_threshold
Rhizobium pusense	strain=LMG 25623	GCA_900102105.1	648995	648995	type	True	86.8906	1318	1949	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.7738	623	1949	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.1828	636	1949	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.1597	694	1949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:12,792] [INFO] DFAST Taxonomy check result was written to GCF_010669145.1_ASM1066914v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:12,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:12,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:12,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/checkm_data
[2024-01-24 14:40:12,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:12,867] [INFO] Task started: CheckM
[2024-01-24 14:40:12,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010669145.1_ASM1066914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010669145.1_ASM1066914v1_genomic.fna/checkm_input GCF_010669145.1_ASM1066914v1_genomic.fna/checkm_result
[2024-01-24 14:41:07,804] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:07,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:07,826] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:07,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:07,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010669145.1_ASM1066914v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:07,827] [INFO] Task started: Blastn
[2024-01-24 14:41:07,831] [INFO] Running command: blastn -query GCF_010669145.1_ASM1066914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f616759-4fc6-47de-888b-4b8958aea6c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_010669145.1_ASM1066914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:09,882] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:09,887] [INFO] Selected 11 target genomes.
[2024-01-24 14:41:09,887] [INFO] Target genome list was writen to GCF_010669145.1_ASM1066914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:09,898] [INFO] Task started: fastANI
[2024-01-24 14:41:09,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg639c1fff-8e60-4f5e-af0b-34adddbc08d6/GCF_010669145.1_ASM1066914v1_genomic.fna.gz --refList GCF_010669145.1_ASM1066914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010669145.1_ASM1066914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:25,891] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:25,904] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:25,905] [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_010669145.1	s__Agrobacterium oryzihabitans	100.0	1938	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	conclusive
GCF_900012615.1	s__Agrobacterium sp900012615	92.3377	1453	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	89.9727	1353	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949865.1	s__Agrobacterium nepotum	89.5199	1306	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649785.1	s__Agrobacterium fabacearum	89.2374	1379	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.40	96.96	0.89	0.76	243	-
GCF_005221385.1	s__Agrobacterium sp900013535	89.0666	1436	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.00	98.18	0.90	0.86	7	-
GCF_002943835.1	s__Agrobacterium deltaense	89.0657	1402	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCF_001541315.1	s__Agrobacterium tumefaciens	88.9182	1394	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	88.763	1400	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	88.5218	1293	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005221325.1	s__Agrobacterium sp900012625	88.1394	1367	1949	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.19	97.65	0.98	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:25,906] [INFO] GTDB search result was written to GCF_010669145.1_ASM1066914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:25,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:25,912] [INFO] DFAST_QC result json was written to GCF_010669145.1_ASM1066914v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:25,912] [INFO] DFAST_QC completed!
[2024-01-24 14:41:25,912] [INFO] Total running time: 0h1m52s