[2024-01-24 13:18:26,092] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,093] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference
[2024-01-24 13:18:27,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,477] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg11531f5a-f28f-494e-af78-591da0016606/GCF_902652675.1_B191_genomic.fna.gz | prodigal -d GCF_902652675.1_B191_genomic.fna/cds.fna -a GCF_902652675.1_B191_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:31,731] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:31,731] [INFO] Task started: HMMsearch
[2024-01-24 13:18:31,731] [INFO] Running command: hmmsearch --tblout GCF_902652675.1_B191_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/reference_markers.hmm GCF_902652675.1_B191_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:31,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:31,992] [INFO] Found 6/6 markers.
[2024-01-24 13:18:32,015] [INFO] Query marker FASTA was written to GCF_902652675.1_B191_genomic.fna/markers.fasta
[2024-01-24 13:18:32,015] [INFO] Task started: Blastn
[2024-01-24 13:18:32,015] [INFO] Running command: blastn -query GCF_902652675.1_B191_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/reference_markers.fasta -out GCF_902652675.1_B191_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:32,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:32,669] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:32,670] [INFO] Target genome list was writen to GCF_902652675.1_B191_genomic.fna/target_genomes.txt
[2024-01-24 13:18:32,688] [INFO] Task started: fastANI
[2024-01-24 13:18:32,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg11531f5a-f28f-494e-af78-591da0016606/GCF_902652675.1_B191_genomic.fna.gz --refList GCF_902652675.1_B191_genomic.fna/target_genomes.txt --output GCF_902652675.1_B191_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:42,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:42,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:42,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:42,311] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:42,311] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:42,311] [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 birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	86.1818	489	588	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	85.2871	487	588	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	85.275	492	588	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	85.21	459	588	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	85.1525	458	588	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	85.1315	460	588	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	85.1099	483	588	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	85.0257	482	588	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	84.9571	471	588	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.3324	477	588	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.3138	474	588	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.3034	467	588	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	84.2995	474	588	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	84.2357	448	588	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	84.2298	486	588	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	84.142	516	588	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	84.0997	456	588	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	84.0714	518	588	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	84.0536	473	588	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	84.0515	476	588	95	below_threshold
Bartonella grahamii	strain=ATCC 700132	GCA_000518085.1	33045	33045	type	True	84.0257	503	588	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	83.7434	500	588	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.4151	412	588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,313] [INFO] DFAST Taxonomy check result was written to GCF_902652675.1_B191_genomic.fna/tc_result.tsv
[2024-01-24 13:18:42,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:42,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:42,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/checkm_data
[2024-01-24 13:18:42,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:42,338] [INFO] Task started: CheckM
[2024-01-24 13:18:42,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902652675.1_B191_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902652675.1_B191_genomic.fna/checkm_input GCF_902652675.1_B191_genomic.fna/checkm_result
[2024-01-24 13:19:03,059] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:03,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,078] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:03,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:03,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902652675.1_B191_genomic.fna/markers.fasta)
[2024-01-24 13:19:03,080] [INFO] Task started: Blastn
[2024-01-24 13:19:03,080] [INFO] Running command: blastn -query GCF_902652675.1_B191_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0bac87c-0e2c-4278-874c-430d41eda501/dqc_reference/reference_markers_gtdb.fasta -out GCF_902652675.1_B191_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:04,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:04,164] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:04,165] [INFO] Target genome list was writen to GCF_902652675.1_B191_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:04,172] [INFO] Task started: fastANI
[2024-01-24 13:19:04,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg11531f5a-f28f-494e-af78-591da0016606/GCF_902652675.1_B191_genomic.fna.gz --refList GCF_902652675.1_B191_genomic.fna/target_genomes_gtdb.txt --output GCF_902652675.1_B191_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:08,923] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:08,933] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:08,933] [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_000278115.1	s__Bartonella sp000278115	97.6826	571	588	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	conclusive
GCF_000278295.1	s__Bartonella taylorii	91.8373	542	588	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_902825155.1	s__Bartonella taylorii_A	90.7343	521	588	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_000273375.1	s__Bartonella birtlesii	86.1818	489	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.71	99.25	0.98	0.95	6	-
GCF_902825235.1	s__Bartonella vinsonii	85.3663	508	588	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_000278235.1	s__Bartonella arupensis	85.2704	488	588	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_014203215.1	s__Bartonella callosciuri	85.2069	460	588	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_013388295.1	s__Bartonella alsatica	85.1153	460	588	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	84.3908	496	588	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_009936175.1	s__Bartonella quintana	84.2127	444	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.46	98.37	0.99	0.97	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,934] [INFO] GTDB search result was written to GCF_902652675.1_B191_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:08,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:08,938] [INFO] DFAST_QC result json was written to GCF_902652675.1_B191_genomic.fna/dqc_result.json
[2024-01-24 13:19:08,939] [INFO] DFAST_QC completed!
[2024-01-24 13:19:08,939] [INFO] Total running time: 0h0m43s