[2024-01-24 14:39:45,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,365] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg90efcc72-ded3-425e-9588-af37102f2397/GCF_003149535.1_ASM314953v1_genomic.fna.gz | prodigal -d GCF_003149535.1_ASM314953v1_genomic.fna/cds.fna -a GCF_003149535.1_ASM314953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:00,318] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:00,319] [INFO] Task started: HMMsearch
[2024-01-24 14:40:00,319] [INFO] Running command: hmmsearch --tblout GCF_003149535.1_ASM314953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/reference_markers.hmm GCF_003149535.1_ASM314953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:00,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:00,607] [INFO] Found 6/6 markers.
[2024-01-24 14:40:00,651] [INFO] Query marker FASTA was written to GCF_003149535.1_ASM314953v1_genomic.fna/markers.fasta
[2024-01-24 14:40:00,651] [INFO] Task started: Blastn
[2024-01-24 14:40:00,651] [INFO] Running command: blastn -query GCF_003149535.1_ASM314953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/reference_markers.fasta -out GCF_003149535.1_ASM314953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:01,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:01,514] [INFO] Selected 27 target genomes.
[2024-01-24 14:40:01,515] [INFO] Target genome list was writen to GCF_003149535.1_ASM314953v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:01,526] [INFO] Task started: fastANI
[2024-01-24 14:40:01,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg90efcc72-ded3-425e-9588-af37102f2397/GCF_003149535.1_ASM314953v1_genomic.fna.gz --refList GCF_003149535.1_ASM314953v1_genomic.fna/target_genomes.txt --output GCF_003149535.1_ASM314953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:23,367] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:23,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:23,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:23,393] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:23,394] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:23,394] [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
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	81.5937	682	1260	95	below_threshold
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	81.5521	679	1260	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	81.1627	606	1260	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	81.1613	635	1260	95	below_threshold
Brucella suis	strain=1330	GCA_000223195.1	29461	29461	suspected-type	True	81.1476	608	1260	95	below_threshold
Brucella suis	strain=NCTC10316	GCA_900460605.1	29461	29461	suspected-type	True	81.1178	609	1260	95	below_threshold
Brucella abortus	strain=NCTC10093	GCA_900446005.1	235	235	type	True	81.106	613	1260	95	below_threshold
Brucella inopinata	strain=BO1	GCA_000182725.1	1218315	1218315	type	True	81.1036	601	1260	95	below_threshold
Brucella abortus	strain=544	GCA_000369945.1	235	235	type	True	81.0805	602	1260	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	81.0647	596	1260	95	below_threshold
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	81.0315	612	1260	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	81.0292	642	1260	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	80.9536	655	1260	95	below_threshold
Brucella haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	80.8073	674	1260	95	below_threshold
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	80.8065	632	1260	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	80.1714	637	1260	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	80.139	632	1260	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	79.7246	621	1260	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	79.6494	597	1260	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	77.6952	291	1260	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	77.5582	254	1260	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.4976	276	1260	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.3816	177	1260	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.3267	270	1260	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.2079	233	1260	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.1734	249	1260	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.6952	165	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:23,396] [INFO] DFAST Taxonomy check result was written to GCF_003149535.1_ASM314953v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:23,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:23,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:23,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/checkm_data
[2024-01-24 14:40:23,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:23,438] [INFO] Task started: CheckM
[2024-01-24 14:40:23,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149535.1_ASM314953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149535.1_ASM314953v1_genomic.fna/checkm_input GCF_003149535.1_ASM314953v1_genomic.fna/checkm_result
[2024-01-24 14:41:02,266] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:02,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:02,291] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:02,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:02,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149535.1_ASM314953v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:02,294] [INFO] Task started: Blastn
[2024-01-24 14:41:02,294] [INFO] Running command: blastn -query GCF_003149535.1_ASM314953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463c3e43-53d6-4e0d-9e1d-281a5baf1208/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149535.1_ASM314953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:03,864] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:03,868] [INFO] Selected 13 target genomes.
[2024-01-24 14:41:03,868] [INFO] Target genome list was writen to GCF_003149535.1_ASM314953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:03,879] [INFO] Task started: fastANI
[2024-01-24 14:41:03,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg90efcc72-ded3-425e-9588-af37102f2397/GCF_003149535.1_ASM314953v1_genomic.fna.gz --refList GCF_003149535.1_ASM314953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149535.1_ASM314953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:16,417] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:16,435] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:16,435] [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_003149535.1	s__Falsochrobactrum shanghaiense	100.0	1257	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019100495.1	s__Falsochrobactrum sp019100495	84.6946	844	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Falsochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	81.7901	697	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199265.1	s__Ochrobactrum_C daejeonensis	81.1814	632	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_C	95.0	99.74	99.74	0.99	0.99	2	-
GCF_000007125.1	s__Brucella melitensis	81.0471	611	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Brucella	95.0	99.71	97.51	0.99	0.88	877	-
GCA_900473915.1	s__Ochrobactrum sp900473915	80.9223	668	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014253075.1	s__JACLZJ01 sp014253075	80.8314	635	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__JACLZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938105.1	s__Ochrobactrum_B haematophila	80.822	672	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.61	97.38	0.92	0.84	3	-
GCF_008932295.1	s__Ochrobactrum tritici	80.8109	632	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.18	96.73	0.91	0.84	6	-
GCF_014138095.1	s__Ochrobactrum_B sp014138095	80.7421	658	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898995.1	s__63-22 sp001898995	80.1947	535	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003049685.1	s__Ochrobactrum_A pituitosa	80.1835	637	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	98.27	97.05	0.91	0.82	14	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	79.7229	622	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:16,437] [INFO] GTDB search result was written to GCF_003149535.1_ASM314953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:16,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:16,441] [INFO] DFAST_QC result json was written to GCF_003149535.1_ASM314953v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:16,442] [INFO] DFAST_QC completed!
[2024-01-24 14:41:16,442] [INFO] Total running time: 0h1m31s