[2024-01-25 18:11:35,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference
[2024-01-25 18:11:36,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,884] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg2075bf94-bc67-4add-83d8-f8293358e7b6/GCF_000739935.1_ASM73993v1_genomic.fna.gz | prodigal -d GCF_000739935.1_ASM73993v1_genomic.fna/cds.fna -a GCF_000739935.1_ASM73993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:51,354] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:51,354] [INFO] Task started: HMMsearch
[2024-01-25 18:11:51,354] [INFO] Running command: hmmsearch --tblout GCF_000739935.1_ASM73993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/reference_markers.hmm GCF_000739935.1_ASM73993v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:51,643] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:51,644] [INFO] Found 6/6 markers.
[2024-01-25 18:11:51,688] [INFO] Query marker FASTA was written to GCF_000739935.1_ASM73993v1_genomic.fna/markers.fasta
[2024-01-25 18:11:51,688] [INFO] Task started: Blastn
[2024-01-25 18:11:51,688] [INFO] Running command: blastn -query GCF_000739935.1_ASM73993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/reference_markers.fasta -out GCF_000739935.1_ASM73993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:52,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:52,515] [INFO] Selected 10 target genomes.
[2024-01-25 18:11:52,515] [INFO] Target genome list was writen to GCF_000739935.1_ASM73993v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:52,527] [INFO] Task started: fastANI
[2024-01-25 18:11:52,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg2075bf94-bc67-4add-83d8-f8293358e7b6/GCF_000739935.1_ASM73993v1_genomic.fna.gz --refList GCF_000739935.1_ASM73993v1_genomic.fna/target_genomes.txt --output GCF_000739935.1_ASM73993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:03,783] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:03,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:03,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:03,791] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:12:03,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:03,791] [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
Agrobacterium rubi	strain=NBRC 13261	GCA_000739935.1	28099	28099	type	True	100.0	1732	1733	95	conclusive
Agrobacterium rubi	strain=DSM 6772	GCA_017873055.1	28099	28099	type	True	99.9974	1725	1733	95	conclusive
Agrobacterium rosae	strain=NCPPB 1650	GCA_002915175.1	1972867	1972867	type	True	85.6334	1206	1733	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	84.9822	1198	1733	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	84.9776	1197	1733	95	below_threshold
Agrobacterium bohemicum	strain=R90	GCA_002896715.1	2052828	2052828	type	True	84.1428	1049	1733	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	80.4324	811	1733	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.2829	457	1733	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.0352	439	1733	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.9701	361	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:03,793] [INFO] DFAST Taxonomy check result was written to GCF_000739935.1_ASM73993v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:03,795] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:03,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:03,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/checkm_data
[2024-01-25 18:12:03,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:03,845] [INFO] Task started: CheckM
[2024-01-25 18:12:03,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739935.1_ASM73993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739935.1_ASM73993v1_genomic.fna/checkm_input GCF_000739935.1_ASM73993v1_genomic.fna/checkm_result
[2024-01-25 18:12:46,853] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:46,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:46,875] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:46,875] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:46,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739935.1_ASM73993v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:46,876] [INFO] Task started: Blastn
[2024-01-25 18:12:46,876] [INFO] Running command: blastn -query GCF_000739935.1_ASM73993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70779a40-57c1-4e07-9d5a-e06ca2c8022c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739935.1_ASM73993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:48,527] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:48,530] [INFO] Selected 9 target genomes.
[2024-01-25 18:12:48,530] [INFO] Target genome list was writen to GCF_000739935.1_ASM73993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:48,561] [INFO] Task started: fastANI
[2024-01-25 18:12:48,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg2075bf94-bc67-4add-83d8-f8293358e7b6/GCF_000739935.1_ASM73993v1_genomic.fna.gz --refList GCF_000739935.1_ASM73993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739935.1_ASM73993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:00,119] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:00,126] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:00,126] [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_000739935.1	s__Agrobacterium rubi	100.0	1732	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.45	95.90	0.89	0.87	10	conclusive
GCA_900468015.1	s__Agrobacterium sp900468015	87.3213	1100	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	95.47	95.47	0.86	0.86	2	-
GCF_002915175.1	s__Agrobacterium rosae	85.638	1205	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.78	95.28	0.91	0.82	8	-
GCA_900473205.1	s__Agrobacterium sp900473205	85.3801	1104	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001422245.1	s__Agrobacterium sp001422245	85.2129	1042	1733	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	84.9753	1197	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCA_900472925.1	s__Agrobacterium sp900472925	84.5001	1059	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896715.1	s__Agrobacterium bohemicum	84.1361	1050	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.81	99.81	1.00	1.00	2	-
GCF_001541315.1	s__Agrobacterium tumefaciens	80.4116	815	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:00,127] [INFO] GTDB search result was written to GCF_000739935.1_ASM73993v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:00,128] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:00,130] [INFO] DFAST_QC result json was written to GCF_000739935.1_ASM73993v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:00,130] [INFO] DFAST_QC completed!
[2024-01-25 18:13:00,131] [INFO] Total running time: 0h1m24s