[2024-01-24 13:36:45,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,537] [INFO] DQC Reference Directory: /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference
[2024-01-24 13:36:46,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,885] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,886] [INFO] Running command: gunzip -c /var/lib/cwl/stga6074763-e856-4645-8b0f-fe69bb9fea87/GCF_000196435.1_ASM19643v1_genomic.fna.gz | prodigal -d GCF_000196435.1_ASM19643v1_genomic.fna/cds.fna -a GCF_000196435.1_ASM19643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:53,335] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:53,335] [INFO] Task started: HMMsearch
[2024-01-24 13:36:53,336] [INFO] Running command: hmmsearch --tblout GCF_000196435.1_ASM19643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/reference_markers.hmm GCF_000196435.1_ASM19643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:53,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:53,553] [INFO] Found 6/6 markers.
[2024-01-24 13:36:53,575] [INFO] Query marker FASTA was written to GCF_000196435.1_ASM19643v1_genomic.fna/markers.fasta
[2024-01-24 13:36:53,576] [INFO] Task started: Blastn
[2024-01-24 13:36:53,576] [INFO] Running command: blastn -query GCF_000196435.1_ASM19643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/reference_markers.fasta -out GCF_000196435.1_ASM19643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:54,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:54,200] [INFO] Selected 23 target genomes.
[2024-01-24 13:36:54,201] [INFO] Target genome list was writen to GCF_000196435.1_ASM19643v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:54,257] [INFO] Task started: fastANI
[2024-01-24 13:36:54,257] [INFO] Running command: fastANI --query /var/lib/cwl/stga6074763-e856-4645-8b0f-fe69bb9fea87/GCF_000196435.1_ASM19643v1_genomic.fna.gz --refList GCF_000196435.1_ASM19643v1_genomic.fna/target_genomes.txt --output GCF_000196435.1_ASM19643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,358] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:07,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:07,358] [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 tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	100.0	858	880	95	conclusive
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	93.4964	673	880	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	90.2809	602	880	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	90.2633	599	880	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	90.2423	563	880	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	90.2103	613	880	95	below_threshold
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	90.0465	630	880	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	89.2849	653	880	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	89.0992	525	880	95	below_threshold
Bartonella grahamii	strain=ATCC 700132	GCA_000518085.1	33045	33045	type	True	88.9244	620	880	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	88.8024	671	880	95	below_threshold
Bartonella massiliensis	strain=OS09	GCA_902150025.1	929795	929795	type	True	88.7847	633	880	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.9171	504	880	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.8562	500	880	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	82.5837	493	880	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	82.5019	495	880	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	82.3024	466	880	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	82.0766	478	880	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	82.0266	468	880	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	82.0082	464	880	95	below_threshold
Bartonella doshiae	strain=CCUG 50770	GCA_902728115.1	33044	33044	type	True	82.0014	463	880	95	below_threshold
Bartonella rattaustraliani	strain=AUST/NH4	GCA_000312565.2	481139	481139	type	True	81.7509	506	880	95	below_threshold
Bartonella bacilliformis	strain=KC583; ATCC 35685	GCA_000015445.1	774	774	type	True	78.8806	269	880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,360] [INFO] DFAST Taxonomy check result was written to GCF_000196435.1_ASM19643v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/checkm_data
[2024-01-24 13:37:07,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:07,451] [INFO] Task started: CheckM
[2024-01-24 13:37:07,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196435.1_ASM19643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196435.1_ASM19643v1_genomic.fna/checkm_input GCF_000196435.1_ASM19643v1_genomic.fna/checkm_result
[2024-01-24 13:37:33,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:33,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:33,403] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:33,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:33,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196435.1_ASM19643v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:33,404] [INFO] Task started: Blastn
[2024-01-24 13:37:33,404] [INFO] Running command: blastn -query GCF_000196435.1_ASM19643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge802b8e0-8dd7-4814-9a80-a597dc12aedb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196435.1_ASM19643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,214] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,217] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:34,218] [INFO] Target genome list was writen to GCF_000196435.1_ASM19643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:34,234] [INFO] Task started: fastANI
[2024-01-24 13:37:34,235] [INFO] Running command: fastANI --query /var/lib/cwl/stga6074763-e856-4645-8b0f-fe69bb9fea87/GCF_000196435.1_ASM19643v1_genomic.fna.gz --refList GCF_000196435.1_ASM19643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196435.1_ASM19643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:42,260] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:42,270] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:42,271] [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_000196435.1	s__Bartonella tribocorum	100.0	857	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.92	99.90	0.97	0.95	3	conclusive
GCF_003606325.2	s__Bartonella kosoyi	93.5398	671	880	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_002777915.1	s__Bartonella tribocorum_A	92.4754	639	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018155095.1	s__Bartonella queenslandensis_B	92.0269	617	880	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_000312585.1	s__Bartonella queenslandensis_A	91.5103	625	880	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_002778015.1	s__Bartonella tribocorum_B	91.1321	594	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000518165.1	s__Bartonella elizabethae	90.2808	598	880	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.20	95.98	0.98	0.96	7	-
GCF_000518085.1	s__Bartonella grahamii	88.9016	623	880	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_902150025.1	s__Bartonella massiliensis	88.7752	634	880	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_000312565.1	s__Bartonella rattaustraliani	81.7454	504	880	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 13:37:42,273] [INFO] GTDB search result was written to GCF_000196435.1_ASM19643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:42,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:42,278] [INFO] DFAST_QC result json was written to GCF_000196435.1_ASM19643v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:42,279] [INFO] DFAST_QC completed!
[2024-01-24 13:37:42,279] [INFO] Total running time: 0h0m57s