[2024-01-24 14:14:31,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,979] [INFO] DQC Reference Directory: /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference
[2024-01-24 14:14:33,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,204] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,204] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbb69473-0810-44e1-98a6-a678ef4831d3/GCF_005145045.1_ASM514504v1_genomic.fna.gz | prodigal -d GCF_005145045.1_ASM514504v1_genomic.fna/cds.fna -a GCF_005145045.1_ASM514504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:48,952] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:48,953] [INFO] Task started: HMMsearch
[2024-01-24 14:14:48,953] [INFO] Running command: hmmsearch --tblout GCF_005145045.1_ASM514504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/reference_markers.hmm GCF_005145045.1_ASM514504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:49,320] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:49,321] [INFO] Found 6/6 markers.
[2024-01-24 14:14:49,367] [INFO] Query marker FASTA was written to GCF_005145045.1_ASM514504v1_genomic.fna/markers.fasta
[2024-01-24 14:14:49,367] [INFO] Task started: Blastn
[2024-01-24 14:14:49,367] [INFO] Running command: blastn -query GCF_005145045.1_ASM514504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/reference_markers.fasta -out GCF_005145045.1_ASM514504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:50,250] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:50,253] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:50,254] [INFO] Target genome list was writen to GCF_005145045.1_ASM514504v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:50,275] [INFO] Task started: fastANI
[2024-01-24 14:14:50,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbb69473-0810-44e1-98a6-a678ef4831d3/GCF_005145045.1_ASM514504v1_genomic.fna.gz --refList GCF_005145045.1_ASM514504v1_genomic.fna/target_genomes.txt --output GCF_005145045.1_ASM514504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:06,843] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:06,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:06,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:06,860] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:06,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:06,860] [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 larrymoorei	strain=CFBP5473	GCA_005145045.1	160699	160699	type	True	100.0	1747	1751	95	conclusive
Agrobacterium larrymoorei	strain=ATCC 51759	GCA_000518585.1	160699	160699	type	True	99.9566	1678	1751	95	conclusive
Agrobacterium cavarae	strain=RZME10	GCA_004310285.1	2528239	2528239	type	True	82.4695	983	1751	95	below_threshold
Agrobacterium rubi	strain=DSM 6772	GCA_017873055.1	28099	28099	type	True	81.4965	936	1751	95	below_threshold
Agrobacterium rosae	strain=NCPPB 1650	GCA_002915175.1	1972867	1972867	type	True	81.445	947	1751	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	80.9933	857	1751	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	80.857	896	1751	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	80.7628	835	1751	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	80.7591	886	1751	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	80.7455	836	1751	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	80.744	892	1751	95	below_threshold
Agrobacterium bohemicum	strain=R90	GCA_002896715.1	2052828	2052828	type	True	80.7299	855	1751	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	80.7286	854	1751	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	80.6127	825	1751	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.8395	508	1751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:06,862] [INFO] DFAST Taxonomy check result was written to GCF_005145045.1_ASM514504v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:06,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:06,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:06,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/checkm_data
[2024-01-24 14:15:06,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:06,918] [INFO] Task started: CheckM
[2024-01-24 14:15:06,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005145045.1_ASM514504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005145045.1_ASM514504v1_genomic.fna/checkm_input GCF_005145045.1_ASM514504v1_genomic.fna/checkm_result
[2024-01-24 14:15:56,019] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:56,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:56,039] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:56,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:56,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005145045.1_ASM514504v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:56,039] [INFO] Task started: Blastn
[2024-01-24 14:15:56,040] [INFO] Running command: blastn -query GCF_005145045.1_ASM514504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1f7f978-a04d-4bab-8282-43dabc6ac504/dqc_reference/reference_markers_gtdb.fasta -out GCF_005145045.1_ASM514504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:57,756] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:57,760] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:57,760] [INFO] Target genome list was writen to GCF_005145045.1_ASM514504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:57,796] [INFO] Task started: fastANI
[2024-01-24 14:15:57,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbb69473-0810-44e1-98a6-a678ef4831d3/GCF_005145045.1_ASM514504v1_genomic.fna.gz --refList GCF_005145045.1_ASM514504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005145045.1_ASM514504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:23,450] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:23,467] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:23,467] [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_005145045.1	s__Agrobacterium larrymoorei	100.0	1748	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.14	96.28	0.93	0.86	3	conclusive
GCF_013322225.1	s__Agrobacterium larrymoorei_A	84.1407	987	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310285.1	s__Agrobacterium cavarae	82.4671	983	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.31	96.14	0.89	0.86	31	-
GCA_900473205.1	s__Agrobacterium sp900473205	82.2066	991	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002915175.1	s__Agrobacterium rosae	81.4259	949	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.78	95.28	0.91	0.82	8	-
GCF_002943835.1	s__Agrobacterium deltaense	81.0206	890	1751	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	80.7881	882	1751	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	80.7842	841	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.47	97.45	0.92	0.92	3	-
GCA_900468285.1	s__Agrobacterium sp900468285	80.7467	869	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.68	97.44	0.95	0.93	14	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	80.7302	854	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCF_002896715.1	s__Agrobacterium bohemicum	80.7223	856	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.81	99.81	1.00	1.00	2	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	80.6979	871	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005221385.1	s__Agrobacterium sp900013535	80.6839	879	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.00	98.18	0.90	0.86	7	-
GCF_002008225.1	s__Agrobacterium salinitolerans	80.612	825	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	80.4855	867	1751	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	80.4696	841	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013390595.1	s__Agrobacterium sp005938205	79.9687	697	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003597675.1	s__Neorhizobium sp003597675	78.9681	546	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343585.1	s__Neorhizobium sp004343585	78.9154	587	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	78.5197	547	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCF_006335145.1	s__Neorhizobium smilacinae	78.4031	543	1751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:23,469] [INFO] GTDB search result was written to GCF_005145045.1_ASM514504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:23,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:23,474] [INFO] DFAST_QC result json was written to GCF_005145045.1_ASM514504v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:23,474] [INFO] DFAST_QC completed!
[2024-01-24 14:16:23,474] [INFO] Total running time: 0h1m51s