[2024-01-24 13:40:00,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:00,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:00,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference
[2024-01-24 13:40:01,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,609] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a6fec60-e4ec-48d9-8f49-4f7e88e5506d/GCF_000742005.1_ASM74200v1_genomic.fna.gz | prodigal -d GCF_000742005.1_ASM74200v1_genomic.fna/cds.fna -a GCF_000742005.1_ASM74200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:12,130] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:12,131] [INFO] Task started: HMMsearch
[2024-01-24 13:40:12,131] [INFO] Running command: hmmsearch --tblout GCF_000742005.1_ASM74200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/reference_markers.hmm GCF_000742005.1_ASM74200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:12,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:12,385] [INFO] Found 6/6 markers.
[2024-01-24 13:40:12,414] [INFO] Query marker FASTA was written to GCF_000742005.1_ASM74200v1_genomic.fna/markers.fasta
[2024-01-24 13:40:12,414] [INFO] Task started: Blastn
[2024-01-24 13:40:12,414] [INFO] Running command: blastn -query GCF_000742005.1_ASM74200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/reference_markers.fasta -out GCF_000742005.1_ASM74200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:13,226] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:13,230] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:13,230] [INFO] Target genome list was writen to GCF_000742005.1_ASM74200v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:13,240] [INFO] Task started: fastANI
[2024-01-24 13:40:13,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a6fec60-e4ec-48d9-8f49-4f7e88e5506d/GCF_000742005.1_ASM74200v1_genomic.fna.gz --refList GCF_000742005.1_ASM74200v1_genomic.fna/target_genomes.txt --output GCF_000742005.1_ASM74200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:25,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:25,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:25,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:25,983] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {}, {29459: 'Brucella melitensis', 236: 'Brucella ovis', 29460: 'Brucella neotomae', 29461: 'Brucella suis', 36855: 'Brucella canis'}
[2024-01-24 13:40:25,984] [INFO] Found 16 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 13:40:25,984] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:40:25,984] [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 suis	strain=1330	GCA_000742005.1	29461	29461	suspected-type	True	100.0	1097	1097	95	inconclusive
Brucella suis	strain=1330	GCA_000223195.1	29461	29461	suspected-type	True	99.9837	1093	1097	95	inconclusive
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	99.9834	1093	1097	95	inconclusive
Brucella suis	strain=NCTC10316	GCA_900460605.1	29461	29461	suspected-type	True	99.9803	1093	1097	95	inconclusive
Brucella neotomae	strain=5K33	GCA_000742255.1	29460	29460	suspected-type	True	99.7145	1088	1097	95	inconclusive
Brucella ceti	strain=B1/94	GCA_000158775.1	120577	120577	suspected-type	True	99.7069	1091	1097	95	inconclusive
Brucella abortus	strain=544	GCA_000369945.1	235	235	type	True	99.6529	1078	1097	95	inconclusive
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	99.634	1077	1097	95	inconclusive
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	99.6273	1080	1097	95	inconclusive
Brucella melitensis	strain=16M	GCA_000250795.2	29459	29459	suspected-type	True	99.6013	1047	1097	95	inconclusive
Brucella ovis	strain=ATCC 25840	GCA_000016845.1	236	236	type	True	99.5645	1056	1097	95	inconclusive
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.5196	248	1097	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.5093	269	1097	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.487	271	1097	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.2764	229	1097	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.0882	238	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:25,986] [INFO] DFAST Taxonomy check result was written to GCF_000742005.1_ASM74200v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:25,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:25,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:25,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/checkm_data
[2024-01-24 13:40:25,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:26,025] [INFO] Task started: CheckM
[2024-01-24 13:40:26,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000742005.1_ASM74200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000742005.1_ASM74200v1_genomic.fna/checkm_input GCF_000742005.1_ASM74200v1_genomic.fna/checkm_result
[2024-01-24 13:41:01,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:01,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:01,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:01,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000742005.1_ASM74200v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:01,686] [INFO] Task started: Blastn
[2024-01-24 13:41:01,686] [INFO] Running command: blastn -query GCF_000742005.1_ASM74200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2064c7-a333-4dd7-a9a4-df5e3ca4b1e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000742005.1_ASM74200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,176] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:03,176] [INFO] Target genome list was writen to GCF_000742005.1_ASM74200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:03,186] [INFO] Task started: fastANI
[2024-01-24 13:41:03,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a6fec60-e4ec-48d9-8f49-4f7e88e5506d/GCF_000742005.1_ASM74200v1_genomic.fna.gz --refList GCF_000742005.1_ASM74200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000742005.1_ASM74200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:17,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,498] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:17,499] [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_000007125.1	s__Brucella melitensis	99.634	1077	1097	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	conclusive
GCA_900473915.1	s__Ochrobactrum sp900473915	83.3987	774	1097	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_000182645.1	s__Ochrobactrum intermedium	83.3883	778	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.99	97.16	0.92	0.84	56	-
GCF_008932435.1	s__Ochrobactrum pseudintermedium	83.3166	767	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.90	97.85	0.90	0.89	7	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	83.3102	789	1097	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	83.0422	769	1097	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	-
GCA_900470195.1	s__Ochrobactrum sp900470195	82.9951	782	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.22	97.63	0.95	0.85	7	-
GCF_000017405.1	s__Ochrobactrum anthropi	82.9416	779	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.11	96.94	0.89	0.83	55	-
GCF_902825325.1	s__Ochrobactrum sp003176975	82.8809	772	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.64	97.64	0.88	0.88	2	-
GCF_008932295.1	s__Ochrobactrum tritici	82.872	758	1097	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_006376675.1	s__Ochrobactrum pecoris	82.7864	766	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.97	99.94	1.00	1.00	3	-
GCF_005938105.1	s__Ochrobactrum_B haematophila	82.2171	738	1097	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_014253075.1	s__JACLZJ01 sp014253075	81.3501	734	1097	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	-
GCA_900465915.1	s__63-22 sp900465915	80.6563	588	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	97.55	97.55	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,501] [INFO] GTDB search result was written to GCF_000742005.1_ASM74200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:17,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:17,507] [INFO] DFAST_QC result json was written to GCF_000742005.1_ASM74200v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:17,508] [INFO] DFAST_QC completed!
[2024-01-24 13:41:17,508] [INFO] Total running time: 0h1m17s