[2024-01-24 12:53:56,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,850] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference
[2024-01-24 12:53:58,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,103] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg1acaa3c8-3f28-494b-9c45-8c34fb668cec/GCF_000312565.1_ASM31256v2_genomic.fna.gz | prodigal -d GCF_000312565.1_ASM31256v2_genomic.fna/cds.fna -a GCF_000312565.1_ASM31256v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:02,769] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:02,770] [INFO] Task started: HMMsearch
[2024-01-24 12:54:02,770] [INFO] Running command: hmmsearch --tblout GCF_000312565.1_ASM31256v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/reference_markers.hmm GCF_000312565.1_ASM31256v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:02,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:02,999] [INFO] Found 6/6 markers.
[2024-01-24 12:54:03,030] [INFO] Query marker FASTA was written to GCF_000312565.1_ASM31256v2_genomic.fna/markers.fasta
[2024-01-24 12:54:03,031] [INFO] Task started: Blastn
[2024-01-24 12:54:03,031] [INFO] Running command: blastn -query GCF_000312565.1_ASM31256v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/reference_markers.fasta -out GCF_000312565.1_ASM31256v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:03,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:03,656] [INFO] Selected 27 target genomes.
[2024-01-24 12:54:03,657] [INFO] Target genome list was writen to GCF_000312565.1_ASM31256v2_genomic.fna/target_genomes.txt
[2024-01-24 12:54:03,681] [INFO] Task started: fastANI
[2024-01-24 12:54:03,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg1acaa3c8-3f28-494b-9c45-8c34fb668cec/GCF_000312565.1_ASM31256v2_genomic.fna.gz --refList GCF_000312565.1_ASM31256v2_genomic.fna/target_genomes.txt --output GCF_000312565.1_ASM31256v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:14,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:14,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:14,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:14,927] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:14,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:14,928] [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 rattaustraliani	strain=AUST/NH4	GCA_000312565.2	481139	481139	type	True	100.0	660	661	95	conclusive
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	83.1549	463	661	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	82.7962	465	661	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	82.6556	446	661	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	82.5301	440	661	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	82.4561	443	661	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	82.2877	462	661	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	82.2481	453	661	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	82.1585	462	661	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.1534	454	661	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.1324	458	661	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	82.0968	458	661	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	82.0855	457	661	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	82.0664	446	661	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	82.0638	444	661	95	below_threshold
Bartonella senegalensis	strain=OS02	GCA_000312545.1	1468418	1468418	type	True	81.811	466	661	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	81.7912	480	661	95	below_threshold
Bartonella koehlerae subsp. koehlerae	strain=C-29	GCA_000706625.1	1819240	92181	type	True	81.7147	432	661	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	81.6109	481	661	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	81.5843	478	661	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	81.3312	445	661	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	81.2565	422	661	95	below_threshold
Bartonella doshiae	strain=CCUG 50770	GCA_902728115.1	33044	33044	type	True	81.2485	416	661	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	81.2235	426	661	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	81.1985	436	661	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	81.1953	434	661	95	below_threshold
Bartonella bacilliformis	strain=KC583; ATCC 35685	GCA_000015445.1	774	774	type	True	78.8031	260	661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:14,929] [INFO] DFAST Taxonomy check result was written to GCF_000312565.1_ASM31256v2_genomic.fna/tc_result.tsv
[2024-01-24 12:54:14,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:14,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:14,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/checkm_data
[2024-01-24 12:54:14,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:14,954] [INFO] Task started: CheckM
[2024-01-24 12:54:14,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000312565.1_ASM31256v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000312565.1_ASM31256v2_genomic.fna/checkm_input GCF_000312565.1_ASM31256v2_genomic.fna/checkm_result
[2024-01-24 12:54:35,939] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:35,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:35,967] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:35,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:35,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000312565.1_ASM31256v2_genomic.fna/markers.fasta)
[2024-01-24 12:54:35,968] [INFO] Task started: Blastn
[2024-01-24 12:54:35,968] [INFO] Running command: blastn -query GCF_000312565.1_ASM31256v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0e7b0ae-685e-4c3a-962b-dc5456671a5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000312565.1_ASM31256v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:36,760] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:36,769] [INFO] Selected 18 target genomes.
[2024-01-24 12:54:36,770] [INFO] Target genome list was writen to GCF_000312565.1_ASM31256v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:36,784] [INFO] Task started: fastANI
[2024-01-24 12:54:36,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg1acaa3c8-3f28-494b-9c45-8c34fb668cec/GCF_000312565.1_ASM31256v2_genomic.fna.gz --refList GCF_000312565.1_ASM31256v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000312565.1_ASM31256v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:44,950] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:44,964] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:44,964] [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_000312565.1	s__Bartonella rattaustraliani	100.0	660	661	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_014203215.1	s__Bartonella callosciuri	83.1549	463	661	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_902825155.1	s__Bartonella taylorii_A	83.0219	471	661	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_902825145.1	s__Bartonella phoceensis	82.832	463	661	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	82.7514	484	661	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_902825225.1	s__Bartonella berkhoffii	82.6459	446	661	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_902825235.1	s__Bartonella vinsonii	82.5243	479	661	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_000278115.1	s__Bartonella sp000278115	82.4876	490	661	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	82.4522	443	661	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_000312585.1	s__Bartonella queenslandensis_A	82.3095	474	661	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_000312525.1	s__Bartonella florencae	82.2803	463	661	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_000046705.1	s__Bartonella henselae	82.2566	452	661	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_000273375.1	s__Bartonella birtlesii	82.0748	460	661	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_013388295.1	s__Bartonella alsatica	82.0638	444	661	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_009936175.1	s__Bartonella quintana	81.9115	419	661	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_000312545.1	s__Bartonella senegalensis	81.7853	468	661	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_000706625.1	s__Bartonella koehlerae	81.6984	433	661	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_002778015.1	s__Bartonella tribocorum_B	81.3745	460	661	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:44,966] [INFO] GTDB search result was written to GCF_000312565.1_ASM31256v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:44,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:44,971] [INFO] DFAST_QC result json was written to GCF_000312565.1_ASM31256v2_genomic.fna/dqc_result.json
[2024-01-24 12:54:44,971] [INFO] DFAST_QC completed!
[2024-01-24 12:54:44,971] [INFO] Total running time: 0h0m48s