[2023-06-28 18:36:16,352] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:36:16,354] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:36:16,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference
[2023-06-28 18:36:17,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:36:17,547] [INFO] Task started: Prodigal
[2023-06-28 18:36:17,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c6c01ef-d5f2-407d-873b-cd7c4945a2c6/GCA_017308595.1_ASM1730859v1_genomic.fna.gz | prodigal -d GCA_017308595.1_ASM1730859v1_genomic.fna/cds.fna -a GCA_017308595.1_ASM1730859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:36:31,271] [INFO] Task succeeded: Prodigal
[2023-06-28 18:36:31,272] [INFO] Task started: HMMsearch
[2023-06-28 18:36:31,272] [INFO] Running command: hmmsearch --tblout GCA_017308595.1_ASM1730859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/reference_markers.hmm GCA_017308595.1_ASM1730859v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:36:31,562] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:36:31,563] [INFO] Found 6/6 markers.
[2023-06-28 18:36:31,604] [INFO] Query marker FASTA was written to GCA_017308595.1_ASM1730859v1_genomic.fna/markers.fasta
[2023-06-28 18:36:31,604] [INFO] Task started: Blastn
[2023-06-28 18:36:31,604] [INFO] Running command: blastn -query GCA_017308595.1_ASM1730859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/reference_markers.fasta -out GCA_017308595.1_ASM1730859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:36:32,506] [INFO] Task succeeded: Blastn
[2023-06-28 18:36:32,511] [INFO] Selected 13 target genomes.
[2023-06-28 18:36:32,512] [INFO] Target genome list was writen to GCA_017308595.1_ASM1730859v1_genomic.fna/target_genomes.txt
[2023-06-28 18:36:32,514] [INFO] Task started: fastANI
[2023-06-28 18:36:32,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c6c01ef-d5f2-407d-873b-cd7c4945a2c6/GCA_017308595.1_ASM1730859v1_genomic.fna.gz --refList GCA_017308595.1_ASM1730859v1_genomic.fna/target_genomes.txt --output GCA_017308595.1_ASM1730859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:36:48,932] [INFO] Task succeeded: fastANI
[2023-06-28 18:36:48,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:36:48,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:36:48,950] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:36:48,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:36:48,950] [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
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	85.9672	1158	1523	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	84.6752	1138	1523	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	84.2901	1128	1523	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	83.8135	1080	1523	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.4387	712	1523	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	79.4022	507	1523	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.3689	667	1523	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	79.3614	651	1523	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.3316	642	1523	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	79.282	674	1523	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	79.276	672	1523	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	79.1469	674	1523	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	79.0068	573	1523	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:36:48,952] [INFO] DFAST Taxonomy check result was written to GCA_017308595.1_ASM1730859v1_genomic.fna/tc_result.tsv
[2023-06-28 18:36:48,953] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:36:48,953] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:36:48,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/checkm_data
[2023-06-28 18:36:48,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:36:48,998] [INFO] Task started: CheckM
[2023-06-28 18:36:48,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017308595.1_ASM1730859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017308595.1_ASM1730859v1_genomic.fna/checkm_input GCA_017308595.1_ASM1730859v1_genomic.fna/checkm_result
[2023-06-28 18:37:31,772] [INFO] Task succeeded: CheckM
[2023-06-28 18:37:31,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 18:37:31,803] [INFO] ===== Completeness check finished =====
[2023-06-28 18:37:31,803] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:37:31,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017308595.1_ASM1730859v1_genomic.fna/markers.fasta)
[2023-06-28 18:37:31,804] [INFO] Task started: Blastn
[2023-06-28 18:37:31,804] [INFO] Running command: blastn -query GCA_017308595.1_ASM1730859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb4c0dbd-88bd-4df5-8f8c-1cb7189112d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_017308595.1_ASM1730859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:37:33,555] [INFO] Task succeeded: Blastn
[2023-06-28 18:37:33,559] [INFO] Selected 9 target genomes.
[2023-06-28 18:37:33,559] [INFO] Target genome list was writen to GCA_017308595.1_ASM1730859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:37:33,560] [INFO] Task started: fastANI
[2023-06-28 18:37:33,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c6c01ef-d5f2-407d-873b-cd7c4945a2c6/GCA_017308595.1_ASM1730859v1_genomic.fna.gz --refList GCA_017308595.1_ASM1730859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017308595.1_ASM1730859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:37:43,457] [INFO] Task succeeded: fastANI
[2023-06-28 18:37:43,472] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:37:43,472] [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
GCA_017308595.1	s__Afipia sp017308595	100.0	1519	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000336555.1	s__Afipia clevelandensis	85.969	1157	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.84	97.84	0.91	0.91	2	-
GCF_000497575.1	s__Afipia sp000497575	84.6964	1150	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCF_000314675.2	s__Afipia broomeae	84.6596	1139	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCF_014203115.1	s__Afipia massiliensis	84.287	1129	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006325.2	s__Afipia massiliensis_A	84.1821	1089	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308295.2	s__Afipia birgiae	83.8049	1081	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	-
GCA_017474385.1	s__Afipia sp017474385	83.4448	856	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308575.1	s__Afipia sp001897905	82.9253	983	1523	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:37:43,474] [INFO] GTDB search result was written to GCA_017308595.1_ASM1730859v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:37:43,475] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:37:43,479] [INFO] DFAST_QC result json was written to GCA_017308595.1_ASM1730859v1_genomic.fna/dqc_result.json
[2023-06-28 18:37:43,480] [INFO] DFAST_QC completed!
[2023-06-28 18:37:43,480] [INFO] Total running time: 0h1m27s