[2024-01-24 11:05:03,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg398baa0f-cb15-45ed-b3b1-cdef30c03e0c/GCF_019659805.1_ASM1965980v1_genomic.fna.gz | prodigal -d GCF_019659805.1_ASM1965980v1_genomic.fna/cds.fna -a GCF_019659805.1_ASM1965980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:09,558] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:09,558] [INFO] Task started: HMMsearch
[2024-01-24 11:05:09,558] [INFO] Running command: hmmsearch --tblout GCF_019659805.1_ASM1965980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/reference_markers.hmm GCF_019659805.1_ASM1965980v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:09,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:09,875] [INFO] Found 6/6 markers.
[2024-01-24 11:05:09,910] [INFO] Query marker FASTA was written to GCF_019659805.1_ASM1965980v1_genomic.fna/markers.fasta
[2024-01-24 11:05:09,911] [INFO] Task started: Blastn
[2024-01-24 11:05:09,911] [INFO] Running command: blastn -query GCF_019659805.1_ASM1965980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/reference_markers.fasta -out GCF_019659805.1_ASM1965980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:12,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:12,069] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:12,070] [INFO] Target genome list was writen to GCF_019659805.1_ASM1965980v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:12,120] [INFO] Task started: fastANI
[2024-01-24 11:05:12,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg398baa0f-cb15-45ed-b3b1-cdef30c03e0c/GCF_019659805.1_ASM1965980v1_genomic.fna.gz --refList GCF_019659805.1_ASM1965980v1_genomic.fna/target_genomes.txt --output GCF_019659805.1_ASM1965980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:22,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:22,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:22,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:22,241] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:22,241] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:22,242] [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 florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	82.5708	466	637	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	82.5358	403	637	95	below_threshold
Bartonella senegalensis	strain=OS02	GCA_000312545.1	1468418	1468418	type	True	82.5172	441	637	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	82.5003	477	637	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	82.4556	471	637	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.3816	473	637	95	below_threshold
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	82.3761	436	637	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.3679	478	637	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	82.3253	434	637	95	below_threshold
Bartonella grahamii	strain=ATCC 700132	GCA_000518085.1	33045	33045	type	True	82.3242	468	637	95	below_threshold
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	82.3202	433	637	95	below_threshold
Bartonella grahamii	strain=NCTC12860	GCA_900445635.1	33045	33045	type	True	82.3004	513	637	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	82.2723	445	637	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	82.0779	467	637	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	82.0064	462	637	95	below_threshold
Bartonella doshiae	strain=NCTC12862	GCA_900445535.1	33044	33044	type	True	81.9839	453	637	95	below_threshold
Bartonella doshiae	strain=NCTC 12862	GCA_000278155.1	33044	33044	type	True	81.9725	450	637	95	below_threshold
Bartonella doshiae	strain=ATCC 700133	GCA_000526895.1	33044	33044	type	True	81.916	444	637	95	below_threshold
Bartonella doshiae	strain=DSM 102055	GCA_014201435.1	33044	33044	type	True	81.9052	434	637	95	below_threshold
Bartonella koehlerae subsp. koehlerae	strain=C-29	GCA_000706625.1	1819240	92181	type	True	81.8695	429	637	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	81.7604	448	637	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000278215.1	270250	270250	type	True	81.6724	462	637	95	below_threshold
Bartonella rattimassiliensis	strain=15908	GCA_000312605.2	270250	270250	type	True	81.6697	446	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:22,243] [INFO] DFAST Taxonomy check result was written to GCF_019659805.1_ASM1965980v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:22,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:22,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:22,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/checkm_data
[2024-01-24 11:05:22,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:22,267] [INFO] Task started: CheckM
[2024-01-24 11:05:22,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019659805.1_ASM1965980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019659805.1_ASM1965980v1_genomic.fna/checkm_input GCF_019659805.1_ASM1965980v1_genomic.fna/checkm_result
[2024-01-24 11:05:39,676] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:39,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:39,695] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:39,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:39,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019659805.1_ASM1965980v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:39,696] [INFO] Task started: Blastn
[2024-01-24 11:05:39,696] [INFO] Running command: blastn -query GCF_019659805.1_ASM1965980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46267b56-42ab-4571-bb34-35acf83d6123/dqc_reference/reference_markers_gtdb.fasta -out GCF_019659805.1_ASM1965980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:40,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:40,897] [INFO] Selected 19 target genomes.
[2024-01-24 11:05:40,897] [INFO] Target genome list was writen to GCF_019659805.1_ASM1965980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:40,907] [INFO] Task started: fastANI
[2024-01-24 11:05:40,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg398baa0f-cb15-45ed-b3b1-cdef30c03e0c/GCF_019659805.1_ASM1965980v1_genomic.fna.gz --refList GCF_019659805.1_ASM1965980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019659805.1_ASM1965980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:50,115] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:50,127] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:05:50,127] [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_000278295.1	s__Bartonella taylorii	82.7276	478	637	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	82.613	460	637	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	82.5536	467	637	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_000312545.1	s__Bartonella senegalensis	82.4995	442	637	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	82.4864	478	637	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_000046705.1	s__Bartonella henselae	82.458	466	637	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_013388295.1	s__Bartonella alsatica	82.365	433	637	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_000518085.1	s__Bartonella grahamii	82.3392	471	637	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_014203215.1	s__Bartonella callosciuri	82.3258	434	637	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_902825235.1	s__Bartonella vinsonii	82.3202	471	637	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	82.282	456	637	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_902825145.1	s__Bartonella phoceensis	82.2755	445	637	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_902825225.1	s__Bartonella berkhoffii	82.2307	443	637	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_009936175.1	s__Bartonella quintana	82.2297	411	637	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_000278135.1	s__Bartonella washoeensis	82.1887	458	637	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_003606345.3	s__Bartonella krasnovii	82.0475	466	637	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	81.957	452	637	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_000706625.1	s__Bartonella koehlerae	81.8866	428	637	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_000278215.1	s__Bartonella rattimassiliensis	81.7048	460	637	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:50,129] [INFO] GTDB search result was written to GCF_019659805.1_ASM1965980v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:50,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:50,133] [INFO] DFAST_QC result json was written to GCF_019659805.1_ASM1965980v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:50,133] [INFO] DFAST_QC completed!
[2024-01-24 11:05:50,133] [INFO] Total running time: 0h0m46s