[2024-01-25 20:20:35,838] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:35,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:35,839] [INFO] DQC Reference Directory: /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference
[2024-01-25 20:20:36,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:36,958] [INFO] Task started: Prodigal
[2024-01-25 20:20:36,958] [INFO] Running command: gunzip -c /var/lib/cwl/stga0f8890d-3f5f-4678-9043-90104dfc21e6/GCF_002896715.1_ASM289671v1_genomic.fna.gz | prodigal -d GCF_002896715.1_ASM289671v1_genomic.fna/cds.fna -a GCF_002896715.1_ASM289671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:49,876] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:49,876] [INFO] Task started: HMMsearch
[2024-01-25 20:20:49,876] [INFO] Running command: hmmsearch --tblout GCF_002896715.1_ASM289671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/reference_markers.hmm GCF_002896715.1_ASM289671v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:50,160] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:50,162] [INFO] Found 6/6 markers.
[2024-01-25 20:20:50,208] [INFO] Query marker FASTA was written to GCF_002896715.1_ASM289671v1_genomic.fna/markers.fasta
[2024-01-25 20:20:50,208] [INFO] Task started: Blastn
[2024-01-25 20:20:50,208] [INFO] Running command: blastn -query GCF_002896715.1_ASM289671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/reference_markers.fasta -out GCF_002896715.1_ASM289671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:51,041] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:51,044] [INFO] Selected 12 target genomes.
[2024-01-25 20:20:51,044] [INFO] Target genome list was writen to GCF_002896715.1_ASM289671v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:51,055] [INFO] Task started: fastANI
[2024-01-25 20:20:51,055] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f8890d-3f5f-4678-9043-90104dfc21e6/GCF_002896715.1_ASM289671v1_genomic.fna.gz --refList GCF_002896715.1_ASM289671v1_genomic.fna/target_genomes.txt --output GCF_002896715.1_ASM289671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:04,074] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:04,074] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:04,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:04,082] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:04,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:04,083] [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 bohemicum	strain=R90	GCA_002896715.1	2052828	2052828	type	True	100.0	1553	1557	95	conclusive
Agrobacterium rosae	strain=NCPPB 1650	GCA_002915175.1	1972867	1972867	type	True	86.8712	1224	1557	95	below_threshold
Agrobacterium rubi	strain=NBRC 13261	GCA_000739935.1	28099	28099	type	True	84.1351	1033	1557	95	below_threshold
Agrobacterium rubi	strain=DSM 6772	GCA_017873055.1	28099	28099	type	True	84.0489	1061	1557	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	83.1324	960	1557	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	83.1035	973	1557	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	79.8852	741	1557	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	79.8264	736	1557	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	79.7235	750	1557	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	77.7986	395	1557	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.5196	330	1557	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.4854	408	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:04,084] [INFO] DFAST Taxonomy check result was written to GCF_002896715.1_ASM289671v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:04,085] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:04,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:04,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/checkm_data
[2024-01-25 20:21:04,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:04,139] [INFO] Task started: CheckM
[2024-01-25 20:21:04,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002896715.1_ASM289671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002896715.1_ASM289671v1_genomic.fna/checkm_input GCF_002896715.1_ASM289671v1_genomic.fna/checkm_result
[2024-01-25 20:21:43,141] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:43,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:43,163] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:43,163] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:43,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002896715.1_ASM289671v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:43,163] [INFO] Task started: Blastn
[2024-01-25 20:21:43,163] [INFO] Running command: blastn -query GCF_002896715.1_ASM289671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge66047a7-c274-468a-8014-85bbef867fa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002896715.1_ASM289671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:44,660] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:44,663] [INFO] Selected 10 target genomes.
[2024-01-25 20:21:44,664] [INFO] Target genome list was writen to GCF_002896715.1_ASM289671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:44,672] [INFO] Task started: fastANI
[2024-01-25 20:21:44,672] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f8890d-3f5f-4678-9043-90104dfc21e6/GCF_002896715.1_ASM289671v1_genomic.fna.gz --refList GCF_002896715.1_ASM289671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002896715.1_ASM289671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:56,360] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:56,367] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:56,367] [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_002896715.1	s__Agrobacterium bohemicum	100.0	1553	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.81	99.81	1.00	1.00	2	conclusive
GCF_002915175.1	s__Agrobacterium rosae	86.8713	1224	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.78	95.28	0.91	0.82	8	-
GCA_900472925.1	s__Agrobacterium sp900472925	86.6242	1223	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739935.1	s__Agrobacterium rubi	84.1326	1033	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.45	95.90	0.89	0.87	10	-
GCA_900473205.1	s__Agrobacterium sp900473205	83.8863	1093	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900468015.1	s__Agrobacterium sp900468015	83.5385	1063	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	95.47	95.47	0.86	0.86	2	-
GCF_001422245.1	s__Agrobacterium sp001422245	83.335	993	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196515.1	s__Agrobacterium skierniewicense	83.1324	960	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_000834635.1	s__Agrobacterium tumefaciens_C	82.9477	1013	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.02	95.99	0.85	0.85	3	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	79.8761	752	1557	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:56,368] [INFO] GTDB search result was written to GCF_002896715.1_ASM289671v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:56,369] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:56,371] [INFO] DFAST_QC result json was written to GCF_002896715.1_ASM289671v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:56,371] [INFO] DFAST_QC completed!
[2024-01-25 20:21:56,372] [INFO] Total running time: 0h1m21s