[2024-01-24 14:38:49,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference
[2024-01-24 14:38:52,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,377] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c99f406-3bc7-49d0-aabc-b3e37d2c50e8/GCF_900445635.1_51184_C02_genomic.fna.gz | prodigal -d GCF_900445635.1_51184_C02_genomic.fna/cds.fna -a GCF_900445635.1_51184_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:58,263] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:58,263] [INFO] Task started: HMMsearch
[2024-01-24 14:38:58,263] [INFO] Running command: hmmsearch --tblout GCF_900445635.1_51184_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/reference_markers.hmm GCF_900445635.1_51184_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:58,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:58,552] [INFO] Found 6/6 markers.
[2024-01-24 14:38:58,594] [INFO] Query marker FASTA was written to GCF_900445635.1_51184_C02_genomic.fna/markers.fasta
[2024-01-24 14:38:58,595] [INFO] Task started: Blastn
[2024-01-24 14:38:58,595] [INFO] Running command: blastn -query GCF_900445635.1_51184_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/reference_markers.fasta -out GCF_900445635.1_51184_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:59,229] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:59,233] [INFO] Selected 22 target genomes.
[2024-01-24 14:38:59,233] [INFO] Target genome list was writen to GCF_900445635.1_51184_C02_genomic.fna/target_genomes.txt
[2024-01-24 14:38:59,275] [INFO] Task started: fastANI
[2024-01-24 14:38:59,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c99f406-3bc7-49d0-aabc-b3e37d2c50e8/GCF_900445635.1_51184_C02_genomic.fna.gz --refList GCF_900445635.1_51184_C02_genomic.fna/target_genomes.txt --output GCF_900445635.1_51184_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:11,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:11,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:11,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:11,920] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:11,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:11,921] [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 grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	100.0	788	793	95	conclusive
Bartonella grahamii	strain=ATCC 700132	GCA_000518085.1	33045	33045	type	True	99.9242	695	793	95	conclusive
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	88.7595	675	793	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	88.5242	559	793	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	88.4224	647	793	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	88.3241	577	793	95	below_threshold
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	88.2246	604	793	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	88.1511	592	793	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000312605.2	270250	270250	type	True	88.0876	552	793	95	below_threshold
Bartonella fuyuanensis	strain=DSM 100694	GCA_014197255.1	1460968	1460968	type	True	87.8255	561	793	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000278215.1	270250	270250	type	True	87.7226	598	793	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	87.7201	632	793	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	87.0632	526	793	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	83.6042	496	793	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	83.5848	514	793	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	83.5427	551	793	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	83.5418	495	793	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	83.5118	501	793	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	83.4705	514	793	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	83.2333	483	793	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	83.091	516	793	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	83.0058	512	793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:11,923] [INFO] DFAST Taxonomy check result was written to GCF_900445635.1_51184_C02_genomic.fna/tc_result.tsv
[2024-01-24 14:39:11,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:11,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:11,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/checkm_data
[2024-01-24 14:39:11,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:11,955] [INFO] Task started: CheckM
[2024-01-24 14:39:11,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445635.1_51184_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445635.1_51184_C02_genomic.fna/checkm_input GCF_900445635.1_51184_C02_genomic.fna/checkm_result
[2024-01-24 14:39:36,407] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:36,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:36,427] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:36,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:36,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445635.1_51184_C02_genomic.fna/markers.fasta)
[2024-01-24 14:39:36,428] [INFO] Task started: Blastn
[2024-01-24 14:39:36,429] [INFO] Running command: blastn -query GCF_900445635.1_51184_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg30889079-3f15-45bb-b090-61fd6b0e69cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445635.1_51184_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:37,321] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:37,324] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:37,324] [INFO] Target genome list was writen to GCF_900445635.1_51184_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:37,353] [INFO] Task started: fastANI
[2024-01-24 14:39:37,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c99f406-3bc7-49d0-aabc-b3e37d2c50e8/GCF_900445635.1_51184_C02_genomic.fna.gz --refList GCF_900445635.1_51184_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445635.1_51184_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:49,468] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:49,491] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:49,495] [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_000518085.1	s__Bartonella grahamii	99.9052	696	793	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	conclusive
GCF_000196435.1	s__Bartonella tribocorum	88.7776	670	793	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	-
GCF_018155095.1	s__Bartonella queenslandensis_B	88.6136	586	793	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_903679515.1	s__Bartonella gabonensis	88.5224	559	793	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	88.505	622	793	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_003606325.2	s__Bartonella kosoyi	88.417	641	793	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	88.3879	578	793	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	88.3249	577	793	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_000312585.1	s__Bartonella queenslandensis_A	88.1229	601	793	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_014197255.1	s__Bartonella fuyuanensis	87.8593	559	793	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_000278215.1	s__Bartonella rattimassiliensis	87.7558	596	793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.95	99.95	0.99	0.99	2	-
GCF_003606345.3	s__Bartonella krasnovii	87.7062	634	793	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_902150025.1	s__Bartonella massiliensis	87.5715	620	793	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	84.348	548	793	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_902825235.1	s__Bartonella vinsonii	84.2009	534	793	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_000278155.1	s__Bartonella doshiae	83.6017	496	793	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_000312525.1	s__Bartonella florencae	83.5512	550	793	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_000278235.1	s__Bartonella arupensis	83.4636	515	793	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_000278135.1	s__Bartonella washoeensis	83.2691	524	793	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_000312545.1	s__Bartonella senegalensis	82.5699	524	793	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 14:39:49,498] [INFO] GTDB search result was written to GCF_900445635.1_51184_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:49,499] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:49,510] [INFO] DFAST_QC result json was written to GCF_900445635.1_51184_C02_genomic.fna/dqc_result.json
[2024-01-24 14:39:49,511] [INFO] DFAST_QC completed!
[2024-01-24 14:39:49,511] [INFO] Total running time: 0h0m60s