[2024-01-24 12:44:53,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference
[2024-01-24 12:44:55,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,176] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg7329234a-0626-4b83-b6e6-e6054052725c/GCF_003367395.1_ASM336739v1_genomic.fna.gz | prodigal -d GCF_003367395.1_ASM336739v1_genomic.fna/cds.fna -a GCF_003367395.1_ASM336739v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:12,802] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:12,803] [INFO] Task started: HMMsearch
[2024-01-24 12:45:12,803] [INFO] Running command: hmmsearch --tblout GCF_003367395.1_ASM336739v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/reference_markers.hmm GCF_003367395.1_ASM336739v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:13,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:13,120] [INFO] Found 6/6 markers.
[2024-01-24 12:45:13,168] [INFO] Query marker FASTA was written to GCF_003367395.1_ASM336739v1_genomic.fna/markers.fasta
[2024-01-24 12:45:13,168] [INFO] Task started: Blastn
[2024-01-24 12:45:13,168] [INFO] Running command: blastn -query GCF_003367395.1_ASM336739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/reference_markers.fasta -out GCF_003367395.1_ASM336739v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:14,223] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:14,226] [INFO] Selected 28 target genomes.
[2024-01-24 12:45:14,227] [INFO] Target genome list was writen to GCF_003367395.1_ASM336739v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:14,238] [INFO] Task started: fastANI
[2024-01-24 12:45:14,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg7329234a-0626-4b83-b6e6-e6054052725c/GCF_003367395.1_ASM336739v1_genomic.fna.gz --refList GCF_003367395.1_ASM336739v1_genomic.fna/target_genomes.txt --output GCF_003367395.1_ASM336739v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:51,353] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:51,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:51,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:51,377] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:51,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:51,378] [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
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	78.5048	554	1864	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	78.4978	491	1864	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	78.4703	556	1864	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	78.4632	575	1864	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	78.3924	545	1864	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	78.3918	598	1864	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	78.3722	590	1864	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	78.368	583	1864	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	78.3623	602	1864	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	78.3402	601	1864	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	78.3225	608	1864	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	78.2997	605	1864	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	78.2733	551	1864	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	78.2733	589	1864	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.2613	584	1864	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	78.2355	571	1864	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	78.226	515	1864	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	78.2149	489	1864	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	78.1963	554	1864	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	78.1771	582	1864	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	78.1599	595	1864	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	78.1587	547	1864	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	78.1471	387	1864	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	78.0147	526	1864	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	77.8673	396	1864	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	77.8636	392	1864	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	77.8532	394	1864	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.7226	442	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:51,380] [INFO] DFAST Taxonomy check result was written to GCF_003367395.1_ASM336739v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:51,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:51,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:51,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/checkm_data
[2024-01-24 12:45:51,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:51,439] [INFO] Task started: CheckM
[2024-01-24 12:45:51,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367395.1_ASM336739v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367395.1_ASM336739v1_genomic.fna/checkm_input GCF_003367395.1_ASM336739v1_genomic.fna/checkm_result
[2024-01-24 12:46:40,844] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:40,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:40,867] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:40,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:40,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367395.1_ASM336739v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:40,868] [INFO] Task started: Blastn
[2024-01-24 12:46:40,868] [INFO] Running command: blastn -query GCF_003367395.1_ASM336739v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc9ea024-4908-4f60-861a-e08bd8915043/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367395.1_ASM336739v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:43,036] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:43,042] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:43,042] [INFO] Target genome list was writen to GCF_003367395.1_ASM336739v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:43,073] [INFO] Task started: fastANI
[2024-01-24 12:46:43,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg7329234a-0626-4b83-b6e6-e6054052725c/GCF_003367395.1_ASM336739v1_genomic.fna.gz --refList GCF_003367395.1_ASM336739v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367395.1_ASM336739v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:58,432] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:58,448] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:58,448] [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_003367395.1	s__Pseudolabrys taiwanensis	100.0	1864	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018240595.1	s__Pseudolabrys sp018240595	81.1122	868	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	80.8325	804	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	80.7753	774	1864	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	80.6823	829	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005153485.1	s__Pseudolabrys sp005153485	80.5347	831	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878085.1	s__Pseudolabrys sp903878085	80.3678	812	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.95	99.95	0.96	0.96	2	-
GCF_003367195.1	s__Pseudolabrys sp003367195	80.2013	772	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464835.1	s__Pseudolabrys sp001464835	80.1546	714	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839845.1	s__Pseudolabrys sp903839845	80.0891	763	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.70	99.58	0.91	0.88	17	-
GCA_903929045.1	s__Pseudolabrys sp903929045	80.0507	702	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.84	99.84	0.87	0.87	2	-
GCA_903885555.1	s__Pseudolabrys sp903885555	79.9575	720	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.81	99.81	0.96	0.96	2	-
GCA_003152455.1	s__Pseudolabrys sp003152455	79.9112	693	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124795.1	s__Pseudolabrys sp016124795	79.8161	796	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131225.1	s__U87765 sp018131225	78.3083	588	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__U87765	95.0	100.00	100.00	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:58,450] [INFO] GTDB search result was written to GCF_003367395.1_ASM336739v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:58,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:58,456] [INFO] DFAST_QC result json was written to GCF_003367395.1_ASM336739v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:58,457] [INFO] DFAST_QC completed!
[2024-01-24 12:46:58,457] [INFO] Total running time: 0h2m5s