[2023-06-19 11:23:07,717] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:23:07,719] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:23:07,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference
[2023-06-19 11:23:09,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:23:09,122] [INFO] Task started: Prodigal
[2023-06-19 11:23:09,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg25961113-5bc2-4c91-9ff6-7d3982be8a40/GCA_013388965.1_ASM1338896v1_genomic.fna.gz | prodigal -d GCA_013388965.1_ASM1338896v1_genomic.fna/cds.fna -a GCA_013388965.1_ASM1338896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:23:19,697] [INFO] Task succeeded: Prodigal
[2023-06-19 11:23:19,697] [INFO] Task started: HMMsearch
[2023-06-19 11:23:19,697] [INFO] Running command: hmmsearch --tblout GCA_013388965.1_ASM1338896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/reference_markers.hmm GCA_013388965.1_ASM1338896v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:23:20,004] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:23:20,005] [INFO] Found 6/6 markers.
[2023-06-19 11:23:20,044] [INFO] Query marker FASTA was written to GCA_013388965.1_ASM1338896v1_genomic.fna/markers.fasta
[2023-06-19 11:23:20,044] [INFO] Task started: Blastn
[2023-06-19 11:23:20,045] [INFO] Running command: blastn -query GCA_013388965.1_ASM1338896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/reference_markers.fasta -out GCA_013388965.1_ASM1338896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:23:20,980] [INFO] Task succeeded: Blastn
[2023-06-19 11:23:20,988] [INFO] Selected 30 target genomes.
[2023-06-19 11:23:20,988] [INFO] Target genome list was writen to GCA_013388965.1_ASM1338896v1_genomic.fna/target_genomes.txt
[2023-06-19 11:23:20,991] [INFO] Task started: fastANI
[2023-06-19 11:23:20,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg25961113-5bc2-4c91-9ff6-7d3982be8a40/GCA_013388965.1_ASM1338896v1_genomic.fna.gz --refList GCA_013388965.1_ASM1338896v1_genomic.fna/target_genomes.txt --output GCA_013388965.1_ASM1338896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:23:55,060] [INFO] Task succeeded: fastANI
[2023-06-19 11:23:55,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:23:55,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:23:55,086] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:23:55,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 11:23:55,086] [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	78.6877	505	1185	95	below_threshold
Pseudorhodoplanes sinuspersici	strain=CECT 8374	GCA_003610435.1	1235591	1235591	type	True	78.6566	515	1185	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	78.1584	437	1185	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	78.0843	393	1185	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.9762	390	1185	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.958	455	1185	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.9018	365	1185	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	77.8685	480	1185	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	77.854	432	1185	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	77.8502	438	1185	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	77.8452	437	1185	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.8439	438	1185	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	77.828	438	1185	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	77.8131	378	1185	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.8102	411	1185	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.8088	417	1185	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.8087	448	1185	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	77.8081	386	1185	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	77.8007	413	1185	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.7815	418	1185	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	77.7669	410	1185	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.72	308	1185	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.708	404	1185	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.7035	428	1185	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	77.6743	392	1185	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.6716	324	1185	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	77.6119	426	1185	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.45	300	1185	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.336	273	1185	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.9151	334	1185	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 11:23:55,089] [INFO] DFAST Taxonomy check result was written to GCA_013388965.1_ASM1338896v1_genomic.fna/tc_result.tsv
[2023-06-19 11:23:55,089] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:23:55,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:23:55,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/checkm_data
[2023-06-19 11:23:55,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:23:55,131] [INFO] Task started: CheckM
[2023-06-19 11:23:55,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013388965.1_ASM1338896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013388965.1_ASM1338896v1_genomic.fna/checkm_input GCA_013388965.1_ASM1338896v1_genomic.fna/checkm_result
[2023-06-19 11:24:29,474] [INFO] Task succeeded: CheckM
[2023-06-19 11:24:29,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 11:24:29,499] [INFO] ===== Completeness check finished =====
[2023-06-19 11:24:29,500] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:24:29,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013388965.1_ASM1338896v1_genomic.fna/markers.fasta)
[2023-06-19 11:24:29,500] [INFO] Task started: Blastn
[2023-06-19 11:24:29,501] [INFO] Running command: blastn -query GCA_013388965.1_ASM1338896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbb69bc6-bce6-4654-8ebe-1963c3a4094f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013388965.1_ASM1338896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:24:31,126] [INFO] Task succeeded: Blastn
[2023-06-19 11:24:31,131] [INFO] Selected 33 target genomes.
[2023-06-19 11:24:31,131] [INFO] Target genome list was writen to GCA_013388965.1_ASM1338896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:24:31,140] [INFO] Task started: fastANI
[2023-06-19 11:24:31,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg25961113-5bc2-4c91-9ff6-7d3982be8a40/GCA_013388965.1_ASM1338896v1_genomic.fna.gz --refList GCA_013388965.1_ASM1338896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013388965.1_ASM1338896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:25:01,957] [INFO] Task succeeded: fastANI
[2023-06-19 11:25:01,987] [INFO] Found 33 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:25:01,988] [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_013388965.1	s__Pseudorhodoplanes sp013388965	100.0	1170	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	80.2304	579	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCA_008933495.1	s__Pseudorhodoplanes sp008933495	79.9465	407	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	79.0208	465	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899285.1	s__Pseudolabrys sp001899285	78.7942	444	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002119765.1	s__Pseudorhodoplanes sinuspersici	78.7043	503	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003105195.1	s__FEB-22 sp003105195	78.681	419	1185	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_005884685.1	s__PALSA-894 sp005884685	78.6388	459	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869215.1	s__Z2-YC6860 sp016869215	78.4698	464	1185	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_009694215.1	s__Z2-YC6860 sp009694215	78.4298	349	1185	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_018242205.1	s__Pseudolabrys sp018242205	78.2627	435	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367395.1	s__Pseudolabrys taiwanensis	78.2343	459	1185	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	78.1884	393	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297465.1	s__SCUB01 sp004297465	78.1834	374	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__SCUB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	78.1418	438	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCA_009377755.1	s__WHTM01 sp009377755	78.1103	377	1185	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	77.9084	410	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377695.1	s__VAZQ01 sp009377695	77.8972	369	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__VAZQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015165.1	s__Bradyrhizobium denitrificans	77.8889	420	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.10	98.93	0.93	0.90	4	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	77.8596	434	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_009759665.1	s__Bradyrhizobium cajani	77.8511	437	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	-
GCF_000344805.1	s__Bradyrhizobium oligotrophicum	77.8101	412	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129985.1	s__Bradyrhizobium japonicum_H	77.8018	402	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	77.8012	449	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_000239775.1	s__Bradyrhizobium sp000239775	77.7493	403	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.7187	308	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	77.7131	403	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616885.1	s__Bradyrhizobium diazoefficiens_F	77.6746	390	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129425.1	s__Bradyrhizobium erythrophlei_C	77.5579	320	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000516555.1	s__P52-10 sp000516555	77.5319	311	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__P52-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016210825.1	s__JACQTM01 sp016210825	77.4299	256	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JACQTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	77.3468	272	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCA_019075925.1	s__BOG-931 sp019075925	77.0084	249	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__BOG-931	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 11:25:01,990] [INFO] GTDB search result was written to GCA_013388965.1_ASM1338896v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:25:01,991] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:25:02,001] [INFO] DFAST_QC result json was written to GCA_013388965.1_ASM1338896v1_genomic.fna/dqc_result.json
[2023-06-19 11:25:02,001] [INFO] DFAST_QC completed!
[2023-06-19 11:25:02,002] [INFO] Total running time: 0h1m54s