[2024-01-25 18:50:50,508] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference
[2024-01-25 18:50:51,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,615] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg02ea7b03-7b40-427a-8a08-0241971835f9/GCF_021560445.1_ASM2156044v1_genomic.fna.gz | prodigal -d GCF_021560445.1_ASM2156044v1_genomic.fna/cds.fna -a GCF_021560445.1_ASM2156044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:55,758] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:55,758] [INFO] Task started: HMMsearch
[2024-01-25 18:50:55,759] [INFO] Running command: hmmsearch --tblout GCF_021560445.1_ASM2156044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/reference_markers.hmm GCF_021560445.1_ASM2156044v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:55,971] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:55,972] [INFO] Found 6/6 markers.
[2024-01-25 18:50:55,991] [INFO] Query marker FASTA was written to GCF_021560445.1_ASM2156044v1_genomic.fna/markers.fasta
[2024-01-25 18:50:55,991] [INFO] Task started: Blastn
[2024-01-25 18:50:55,991] [INFO] Running command: blastn -query GCF_021560445.1_ASM2156044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/reference_markers.fasta -out GCF_021560445.1_ASM2156044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:56,610] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:56,617] [INFO] Selected 7 target genomes.
[2024-01-25 18:50:56,618] [INFO] Target genome list was writen to GCF_021560445.1_ASM2156044v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:56,623] [INFO] Task started: fastANI
[2024-01-25 18:50:56,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg02ea7b03-7b40-427a-8a08-0241971835f9/GCF_021560445.1_ASM2156044v1_genomic.fna.gz --refList GCF_021560445.1_ASM2156044v1_genomic.fna/target_genomes.txt --output GCF_021560445.1_ASM2156044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:00,535] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:00,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:00,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:00,543] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:51:00,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:00,543] [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 henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	100.0	652	654	95	conclusive
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	99.9991	647	654	95	conclusive
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	99.9981	644	654	95	conclusive
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	99.9931	648	654	95	conclusive
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	99.9804	632	654	95	conclusive
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	82.7587	505	654	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	82.7039	515	654	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:00,545] [INFO] DFAST Taxonomy check result was written to GCF_021560445.1_ASM2156044v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:00,545] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:00,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:00,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/checkm_data
[2024-01-25 18:51:00,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:00,570] [INFO] Task started: CheckM
[2024-01-25 18:51:00,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021560445.1_ASM2156044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021560445.1_ASM2156044v1_genomic.fna/checkm_input GCF_021560445.1_ASM2156044v1_genomic.fna/checkm_result
[2024-01-25 18:51:18,978] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:18,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:19,014] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:19,015] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:19,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021560445.1_ASM2156044v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:19,015] [INFO] Task started: Blastn
[2024-01-25 18:51:19,015] [INFO] Running command: blastn -query GCF_021560445.1_ASM2156044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2e627d-354f-489c-80d7-d1ad6c11b7cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021560445.1_ASM2156044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:19,975] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:19,982] [INFO] Selected 10 target genomes.
[2024-01-25 18:51:19,982] [INFO] Target genome list was writen to GCF_021560445.1_ASM2156044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:19,991] [INFO] Task started: fastANI
[2024-01-25 18:51:19,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg02ea7b03-7b40-427a-8a08-0241971835f9/GCF_021560445.1_ASM2156044v1_genomic.fna.gz --refList GCF_021560445.1_ASM2156044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021560445.1_ASM2156044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:24,786] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:24,793] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:24,793] [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_000046705.1	s__Bartonella henselae	99.9791	635	654	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	conclusive
GCF_000706625.1	s__Bartonella koehlerae	91.8811	560	654	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_000312545.1	s__Bartonella senegalensis	89.3738	551	654	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_009936175.1	s__Bartonella quintana	86.1735	480	654	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_902825155.1	s__Bartonella taylorii_A	84.794	509	654	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_000278135.1	s__Bartonella washoeensis	84.5945	501	654	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_902825145.1	s__Bartonella phoceensis	84.4484	481	654	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_014203215.1	s__Bartonella callosciuri	84.2297	465	654	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	84.1829	482	654	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_000273375.1	s__Bartonella birtlesii	83.7515	495	654	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:24,795] [INFO] GTDB search result was written to GCF_021560445.1_ASM2156044v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:24,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:24,798] [INFO] DFAST_QC result json was written to GCF_021560445.1_ASM2156044v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:24,798] [INFO] DFAST_QC completed!
[2024-01-25 18:51:24,798] [INFO] Total running time: 0h0m34s