[2024-01-24 13:41:10,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference
[2024-01-24 13:41:11,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,349] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,349] [INFO] Running command: gunzip -c /var/lib/cwl/stga261fdd3-06b7-4c1d-9fa8-5b2ae6e1599b/GCF_014203215.1_ASM1420321v1_genomic.fna.gz | prodigal -d GCF_014203215.1_ASM1420321v1_genomic.fna/cds.fna -a GCF_014203215.1_ASM1420321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:14,816] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:14,816] [INFO] Task started: HMMsearch
[2024-01-24 13:41:14,816] [INFO] Running command: hmmsearch --tblout GCF_014203215.1_ASM1420321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/reference_markers.hmm GCF_014203215.1_ASM1420321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:15,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:15,044] [INFO] Found 6/6 markers.
[2024-01-24 13:41:15,060] [INFO] Query marker FASTA was written to GCF_014203215.1_ASM1420321v1_genomic.fna/markers.fasta
[2024-01-24 13:41:15,060] [INFO] Task started: Blastn
[2024-01-24 13:41:15,060] [INFO] Running command: blastn -query GCF_014203215.1_ASM1420321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/reference_markers.fasta -out GCF_014203215.1_ASM1420321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:15,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:15,655] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:15,656] [INFO] Target genome list was writen to GCF_014203215.1_ASM1420321v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:15,660] [INFO] Task started: fastANI
[2024-01-24 13:41:15,660] [INFO] Running command: fastANI --query /var/lib/cwl/stga261fdd3-06b7-4c1d-9fa8-5b2ae6e1599b/GCF_014203215.1_ASM1420321v1_genomic.fna.gz --refList GCF_014203215.1_ASM1420321v1_genomic.fna/target_genomes.txt --output GCF_014203215.1_ASM1420321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,447] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,458] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:22,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:22,458] [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 callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	99.9999	561	563	95	conclusive
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	85.3627	481	563	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	84.9571	472	563	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	84.9555	465	563	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	84.8147	458	563	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	84.7723	465	563	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	84.2552	476	563	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.2188	479	563	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	84.2132	483	563	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.1919	475	563	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.1865	486	563	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	83.9694	480	563	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	83.4749	463	563	95	below_threshold
Bartonella rattaustraliani	strain=AUST/NH4	GCA_000312565.2	481139	481139	type	True	83.154	464	563	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	82.9859	442	563	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	82.9195	454	563	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.3736	394	563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,459] [INFO] DFAST Taxonomy check result was written to GCF_014203215.1_ASM1420321v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/checkm_data
[2024-01-24 13:41:22,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:22,480] [INFO] Task started: CheckM
[2024-01-24 13:41:22,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203215.1_ASM1420321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203215.1_ASM1420321v1_genomic.fna/checkm_input GCF_014203215.1_ASM1420321v1_genomic.fna/checkm_result
[2024-01-24 13:41:38,598] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:38,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,610] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:38,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:38,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203215.1_ASM1420321v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:38,610] [INFO] Task started: Blastn
[2024-01-24 13:41:38,610] [INFO] Running command: blastn -query GCF_014203215.1_ASM1420321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37c2ab7c-1094-41af-9351-655c2d5d3de6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203215.1_ASM1420321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,604] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,606] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:39,607] [INFO] Target genome list was writen to GCF_014203215.1_ASM1420321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:39,614] [INFO] Task started: fastANI
[2024-01-24 13:41:39,614] [INFO] Running command: fastANI --query /var/lib/cwl/stga261fdd3-06b7-4c1d-9fa8-5b2ae6e1599b/GCF_014203215.1_ASM1420321v1_genomic.fna.gz --refList GCF_014203215.1_ASM1420321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203215.1_ASM1420321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,409] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,409] [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_014203215.1	s__Bartonella callosciuri	99.9999	561	563	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	conclusive
GCF_902825155.1	s__Bartonella taylorii_A	85.7254	475	563	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	85.5165	474	563	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	85.3766	480	563	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	85.0592	491	563	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_000278235.1	s__Bartonella arupensis	84.9995	470	563	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_902825235.1	s__Bartonella vinsonii	84.9017	475	563	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	84.7699	465	563	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_000278135.1	s__Bartonella washoeensis	84.2784	473	563	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	84.2198	478	563	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_009936175.1	s__Bartonella quintana	84.1383	445	563	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	-
GCF_000706625.1	s__Bartonella koehlerae	83.9893	467	563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000312525.1	s__Bartonella florencae	83.9509	481	563	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	83.1824	462	563	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_000278155.1	s__Bartonella doshiae	82.9503	452	563	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_003606345.3	s__Bartonella krasnovii	82.4381	465	563	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 13:41:46,410] [INFO] GTDB search result was written to GCF_014203215.1_ASM1420321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,414] [INFO] DFAST_QC result json was written to GCF_014203215.1_ASM1420321v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,414] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,414] [INFO] Total running time: 0h0m36s