[2024-01-24 11:35:23,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference
[2024-01-24 11:35:26,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,244] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,244] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3c69d29-a060-4168-804e-0e14a15a3ed5/GCF_002119765.1_ASM211976v1_genomic.fna.gz | prodigal -d GCF_002119765.1_ASM211976v1_genomic.fna/cds.fna -a GCF_002119765.1_ASM211976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:45,181] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:45,182] [INFO] Task started: HMMsearch
[2024-01-24 11:35:45,182] [INFO] Running command: hmmsearch --tblout GCF_002119765.1_ASM211976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/reference_markers.hmm GCF_002119765.1_ASM211976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:45,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:45,574] [INFO] Found 6/6 markers.
[2024-01-24 11:35:45,626] [INFO] Query marker FASTA was written to GCF_002119765.1_ASM211976v1_genomic.fna/markers.fasta
[2024-01-24 11:35:45,626] [INFO] Task started: Blastn
[2024-01-24 11:35:45,626] [INFO] Running command: blastn -query GCF_002119765.1_ASM211976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/reference_markers.fasta -out GCF_002119765.1_ASM211976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:46,631] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:46,635] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:46,635] [INFO] Target genome list was writen to GCF_002119765.1_ASM211976v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:46,645] [INFO] Task started: fastANI
[2024-01-24 11:35:46,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c69d29-a060-4168-804e-0e14a15a3ed5/GCF_002119765.1_ASM211976v1_genomic.fna.gz --refList GCF_002119765.1_ASM211976v1_genomic.fna/target_genomes.txt --output GCF_002119765.1_ASM211976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:12,119] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:12,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:12,138] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:36:12,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:12,139] [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
Pseudorhodoplanes sinuspersici	strain=RIPI110	GCA_002119765.1	1235591	1235591	type	True	100.0	1990	1990	95	conclusive
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	99.9953	1978	1990	95	conclusive
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	77.9235	341	1990	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	77.8058	459	1990	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.8012	453	1990	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	77.7674	342	1990	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	77.7219	439	1990	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.696	315	1990	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.6654	439	1990	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.6535	413	1990	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	77.6487	325	1990	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	77.6324	332	1990	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	77.612	390	1990	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	77.6043	432	1990	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	77.5986	445	1990	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.579	430	1990	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	77.5215	435	1990	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.4738	299	1990	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.4498	305	1990	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.4121	382	1990	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.3584	334	1990	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.3105	392	1990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,141] [INFO] DFAST Taxonomy check result was written to GCF_002119765.1_ASM211976v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:12,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:12,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:12,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/checkm_data
[2024-01-24 11:36:12,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:12,199] [INFO] Task started: CheckM
[2024-01-24 11:36:12,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002119765.1_ASM211976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002119765.1_ASM211976v1_genomic.fna/checkm_input GCF_002119765.1_ASM211976v1_genomic.fna/checkm_result
[2024-01-24 11:37:09,995] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:09,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:10,022] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:10,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:10,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002119765.1_ASM211976v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:10,023] [INFO] Task started: Blastn
[2024-01-24 11:37:10,023] [INFO] Running command: blastn -query GCF_002119765.1_ASM211976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb1721d-9cda-4ae4-a654-947e2f818a12/dqc_reference/reference_markers_gtdb.fasta -out GCF_002119765.1_ASM211976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:11,959] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:11,964] [INFO] Selected 23 target genomes.
[2024-01-24 11:37:11,964] [INFO] Target genome list was writen to GCF_002119765.1_ASM211976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:11,999] [INFO] Task started: fastANI
[2024-01-24 11:37:11,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3c69d29-a060-4168-804e-0e14a15a3ed5/GCF_002119765.1_ASM211976v1_genomic.fna.gz --refList GCF_002119765.1_ASM211976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002119765.1_ASM211976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:36,736] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:36,761] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:36,761] [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_002119765.1	s__Pseudorhodoplanes sinuspersici	100.0	1990	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_001899285.1	s__Pseudolabrys sp001899285	79.2305	518	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	78.8708	519	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCA_013388965.1	s__Pseudorhodoplanes sp013388965	78.6239	536	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933495.1	s__Pseudorhodoplanes sp008933495	78.6019	365	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	78.3411	421	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240595.1	s__Pseudolabrys sp018240595	78.2444	480	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849615.1	s__Pseudolabrys sp017849615	78.126	464	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694215.1	s__Z2-YC6860 sp009694215	77.905	320	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885555.1	s__Pseudolabrys sp903885555	77.8237	399	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCF_000379145.1	s__Bradyrhizobium elkanii	77.8174	456	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCA_016124795.1	s__Pseudolabrys sp016124795	77.7875	461	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129385.1	s__Bradyrhizobium lablabi_C	77.7142	408	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001982635.1	s__Bradyrhizobium mercantei	77.7103	438	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884685.1	s__PALSA-894 sp005884685	77.6896	425	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295845.1	s__Rhodopseudomonas sp001295845	77.6835	392	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217325.1	s__Rhodopseudomonas faecalis	77.6276	334	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_009720755.1	s__Rhodoplanes serenus	77.6112	343	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	77.61	423	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	77.5579	317	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377755.1	s__WHTM01 sp009377755	77.466	388	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__WHTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	77.2723	389	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169835.1	s__Z2-YC6860 sp003169835	76.8955	221	1990	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	99.86	99.86	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:36,763] [INFO] GTDB search result was written to GCF_002119765.1_ASM211976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:36,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:36,774] [INFO] DFAST_QC result json was written to GCF_002119765.1_ASM211976v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:36,774] [INFO] DFAST_QC completed!
[2024-01-24 11:37:36,774] [INFO] Total running time: 0h2m13s