[2024-01-24 12:13:54,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:54,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:54,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference
[2024-01-24 12:13:57,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,521] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6133623-dfeb-46fb-bfdc-307680660895/GCF_024297065.1_ASM2429706v1_genomic.fna.gz | prodigal -d GCF_024297065.1_ASM2429706v1_genomic.fna/cds.fna -a GCF_024297065.1_ASM2429706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:02,981] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:02,982] [INFO] Task started: HMMsearch
[2024-01-24 12:14:02,982] [INFO] Running command: hmmsearch --tblout GCF_024297065.1_ASM2429706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/reference_markers.hmm GCF_024297065.1_ASM2429706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:03,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:03,362] [INFO] Found 6/6 markers.
[2024-01-24 12:14:03,398] [INFO] Query marker FASTA was written to GCF_024297065.1_ASM2429706v1_genomic.fna/markers.fasta
[2024-01-24 12:14:03,398] [INFO] Task started: Blastn
[2024-01-24 12:14:03,398] [INFO] Running command: blastn -query GCF_024297065.1_ASM2429706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/reference_markers.fasta -out GCF_024297065.1_ASM2429706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:04,339] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:04,343] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:04,343] [INFO] Target genome list was writen to GCF_024297065.1_ASM2429706v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:04,437] [INFO] Task started: fastANI
[2024-01-24 12:14:04,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6133623-dfeb-46fb-bfdc-307680660895/GCF_024297065.1_ASM2429706v1_genomic.fna.gz --refList GCF_024297065.1_ASM2429706v1_genomic.fna/target_genomes.txt --output GCF_024297065.1_ASM2429706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,420] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,435] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:12,435] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:12,436] [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
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	100.0	751	754	95	conclusive
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	85.4255	506	754	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	85.3495	503	754	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	85.3167	521	754	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	85.2713	496	754	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	83.6089	459	754	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	83.5096	475	754	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	82.7586	499	754	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.6902	499	754	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.6688	499	754	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	82.3178	463	754	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	82.2408	478	754	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	82.2388	488	754	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	82.2175	462	754	95	below_threshold
Bartonella rattaustraliani	strain=AUST/NH4	GCA_000312565.2	481139	481139	type	True	81.6773	472	754	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	81.5518	504	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,445] [INFO] DFAST Taxonomy check result was written to GCF_024297065.1_ASM2429706v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/checkm_data
[2024-01-24 12:14:12,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,472] [INFO] Task started: CheckM
[2024-01-24 12:14:12,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024297065.1_ASM2429706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024297065.1_ASM2429706v1_genomic.fna/checkm_input GCF_024297065.1_ASM2429706v1_genomic.fna/checkm_result
[2024-01-24 12:14:36,510] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:36,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:36,537] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:36,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:36,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024297065.1_ASM2429706v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:36,538] [INFO] Task started: Blastn
[2024-01-24 12:14:36,538] [INFO] Running command: blastn -query GCF_024297065.1_ASM2429706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2224aa66-b398-4840-a618-dd6c6efaccf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024297065.1_ASM2429706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:37,648] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:37,654] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:37,654] [INFO] Target genome list was writen to GCF_024297065.1_ASM2429706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:37,674] [INFO] Task started: fastANI
[2024-01-24 12:14:37,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6133623-dfeb-46fb-bfdc-307680660895/GCF_024297065.1_ASM2429706v1_genomic.fna.gz --refList GCF_024297065.1_ASM2429706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024297065.1_ASM2429706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:44,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:44,620] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:14:44,620] [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_902825235.1	s__Bartonella vinsonii	85.4715	535	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902825225.1	s__Bartonella berkhoffii	85.4255	506	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.74	99.27	0.97	0.95	4	-
GCF_000278235.1	s__Bartonella arupensis	85.3019	522	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.53	99.17	0.97	0.95	3	-
GCF_902825155.1	s__Bartonella taylorii_A	84.2278	501	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278295.1	s__Bartonella taylorii	84.0177	533	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.74	97.76	0.94	0.92	5	-
GCF_902825145.1	s__Bartonella phoceensis	83.8209	488	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278115.1	s__Bartonella sp000278115	83.6824	550	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	97.72	97.72	0.97	0.97	2	-
GCF_013388295.1	s__Bartonella alsatica	83.6535	462	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.98	99.96	0.99	0.99	3	-
GCF_000278135.1	s__Bartonella washoeensis	83.0164	513	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.94	98.02	0.92	0.91	3	-
GCF_000046705.1	s__Bartonella henselae	82.6861	513	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.52	98.81	0.98	0.94	29	-
GCF_000518085.1	s__Bartonella grahamii	82.3511	523	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.67	99.54	0.97	0.95	5	-
GCF_000278155.1	s__Bartonella doshiae	82.2819	488	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.97	97.90	0.96	0.87	9	-
GCF_000312565.1	s__Bartonella rattaustraliani	81.7028	469	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:44,623] [INFO] GTDB search result was written to GCF_024297065.1_ASM2429706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:44,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:44,629] [INFO] DFAST_QC result json was written to GCF_024297065.1_ASM2429706v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:44,629] [INFO] DFAST_QC completed!
[2024-01-24 12:14:44,629] [INFO] Total running time: 0h0m50s