[2024-01-24 12:44:43,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference
[2024-01-24 12:44:45,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,116] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg09245fec-694f-4849-9c20-f22d622f87c9/GCF_900446005.1_58116_B01_genomic.fna.gz | prodigal -d GCF_900446005.1_58116_B01_genomic.fna/cds.fna -a GCF_900446005.1_58116_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:55,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:55,908] [INFO] Task started: HMMsearch
[2024-01-24 12:44:55,908] [INFO] Running command: hmmsearch --tblout GCF_900446005.1_58116_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/reference_markers.hmm GCF_900446005.1_58116_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:56,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:56,211] [INFO] Found 6/6 markers.
[2024-01-24 12:44:56,248] [INFO] Query marker FASTA was written to GCF_900446005.1_58116_B01_genomic.fna/markers.fasta
[2024-01-24 12:44:56,248] [INFO] Task started: Blastn
[2024-01-24 12:44:56,248] [INFO] Running command: blastn -query GCF_900446005.1_58116_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/reference_markers.fasta -out GCF_900446005.1_58116_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:57,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:57,156] [INFO] Selected 15 target genomes.
[2024-01-24 12:44:57,156] [INFO] Target genome list was writen to GCF_900446005.1_58116_B01_genomic.fna/target_genomes.txt
[2024-01-24 12:44:57,164] [INFO] Task started: fastANI
[2024-01-24 12:44:57,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg09245fec-694f-4849-9c20-f22d622f87c9/GCF_900446005.1_58116_B01_genomic.fna.gz --refList GCF_900446005.1_58116_B01_genomic.fna/target_genomes.txt --output GCF_900446005.1_58116_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:09,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:09,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:09,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:09,081] [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 12:45:09,082] [INFO] Found 15 fastANI hits (10 hits with ANI > threshold)
[2024-01-24 12:45:09,082] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:45:09,082] [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 abortus	strain=NCTC10093	GCA_900446005.1	235	235	type	True	100.0	1093	1093	95	inconclusive
Brucella abortus	strain=544	GCA_000369945.1	235	235	type	True	99.9861	1091	1093	95	inconclusive
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	99.7065	1078	1093	95	inconclusive
Brucella suis	strain=NCTC10316	GCA_900460605.1	29461	29461	suspected-type	True	99.6852	1078	1093	95	inconclusive
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	99.6776	1074	1093	95	inconclusive
Brucella suis	strain=1330	GCA_000223195.1	29461	29461	suspected-type	True	99.6769	1080	1093	95	inconclusive
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	99.6766	1081	1093	95	inconclusive
Brucella melitensis	strain=16M	GCA_000250795.2	29459	29459	suspected-type	True	99.6733	1040	1093	95	inconclusive
Brucella ceti	strain=B1/94	GCA_000158775.1	120577	120577	suspected-type	True	99.6384	1076	1093	95	inconclusive
Brucella ovis	strain=ATCC 25840	GCA_000016845.1	236	236	type	True	99.5124	1062	1093	95	inconclusive
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.8324	263	1093	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.7003	263	1093	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3889	254	1093	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.0762	232	1093	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.0589	243	1093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:09,084] [INFO] DFAST Taxonomy check result was written to GCF_900446005.1_58116_B01_genomic.fna/tc_result.tsv
[2024-01-24 12:45:09,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:09,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:09,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/checkm_data
[2024-01-24 12:45:09,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:09,120] [INFO] Task started: CheckM
[2024-01-24 12:45:09,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446005.1_58116_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446005.1_58116_B01_genomic.fna/checkm_input GCF_900446005.1_58116_B01_genomic.fna/checkm_result
[2024-01-24 12:45:46,025] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:46,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:46,046] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:46,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:46,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446005.1_58116_B01_genomic.fna/markers.fasta)
[2024-01-24 12:45:46,047] [INFO] Task started: Blastn
[2024-01-24 12:45:46,047] [INFO] Running command: blastn -query GCF_900446005.1_58116_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db7b510-dabb-42ca-9891-c7af31aee59e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446005.1_58116_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:47,461] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:47,465] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:47,465] [INFO] Target genome list was writen to GCF_900446005.1_58116_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:47,492] [INFO] Task started: fastANI
[2024-01-24 12:45:47,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg09245fec-694f-4849-9c20-f22d622f87c9/GCF_900446005.1_58116_B01_genomic.fna.gz --refList GCF_900446005.1_58116_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446005.1_58116_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:59,980] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:59,995] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:59,995] [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	99.7065	1078	1093	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
GCF_000182645.1	s__Ochrobactrum intermedium	83.404	775	1093	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	-
GCA_900473915.1	s__Ochrobactrum sp900473915	83.3307	772	1093	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_003550135.1	s__Ochrobactrum_B haematophila_B	83.3288	771	1093	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_008932435.1	s__Ochrobactrum pseudintermedium	83.2283	763	1093	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	-
GCA_900470195.1	s__Ochrobactrum sp900470195	83.1346	761	1093	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_014199265.1	s__Ochrobactrum_C daejeonensis	82.9996	761	1093	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_000017405.1	s__Ochrobactrum anthropi	82.9966	770	1093	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_008932295.1	s__Ochrobactrum tritici	82.8543	762	1093	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_902825325.1	s__Ochrobactrum sp003176975	82.8312	769	1093	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_005938105.1	s__Ochrobactrum_B haematophila	82.288	726	1093	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	81.3965	727	1093	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_019100495.1	s__Falsochrobactrum sp019100495	80.7623	618	1093	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	-
GCA_900465915.1	s__63-22 sp900465915	80.6809	588	1093	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 12:45:59,997] [INFO] GTDB search result was written to GCF_900446005.1_58116_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:59,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:00,001] [INFO] DFAST_QC result json was written to GCF_900446005.1_58116_B01_genomic.fna/dqc_result.json
[2024-01-24 12:46:00,001] [INFO] DFAST_QC completed!
[2024-01-24 12:46:00,001] [INFO] Total running time: 0h1m16s