[2024-01-24 14:12:47,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference
[2024-01-24 14:12:48,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,825] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,825] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd1a7d32-de08-484c-b44a-0a64e6f936cc/GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna.gz | prodigal -d GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/cds.fna -a GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:53,221] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:53,221] [INFO] Task started: HMMsearch
[2024-01-24 14:12:53,221] [INFO] Running command: hmmsearch --tblout GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/reference_markers.hmm GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:53,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:53,458] [INFO] Found 6/6 markers.
[2024-01-24 14:12:53,477] [INFO] Query marker FASTA was written to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/markers.fasta
[2024-01-24 14:12:53,478] [INFO] Task started: Blastn
[2024-01-24 14:12:53,478] [INFO] Running command: blastn -query GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/markers.fasta -db /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/reference_markers.fasta -out GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:54,064] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:54,068] [INFO] Selected 14 target genomes.
[2024-01-24 14:12:54,069] [INFO] Target genome list was writen to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/target_genomes.txt
[2024-01-24 14:12:54,124] [INFO] Task started: fastANI
[2024-01-24 14:12:54,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1a7d32-de08-484c-b44a-0a64e6f936cc/GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna.gz --refList GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/target_genomes.txt --output GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:00,595] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:00,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:00,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:00,620] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:13:00,620] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:13:00,621] [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 elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	100.0	634	634	95	inconclusive
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	99.95	630	634	95	inconclusive
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	99.9472	620	634	95	inconclusive
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	95.8811	613	634	95	inconclusive
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	94.5869	608	634	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	92.0678	496	634	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	91.5443	590	634	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	82.5438	463	634	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	82.4762	468	634	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	82.2002	456	634	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.0568	486	634	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.0526	472	634	95	below_threshold
Bartonella henselae	strain=FDAARGOS_175	GCA_001525625.2	38323	38323	type	True	82.0336	481	634	95	below_threshold
Bartonella henselae	strain=Houston-1	GCA_000046705.1	38323	38323	type	True	81.9738	494	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:00,622] [INFO] DFAST Taxonomy check result was written to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/tc_result.tsv
[2024-01-24 14:13:00,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:00,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:00,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/checkm_data
[2024-01-24 14:13:00,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:00,650] [INFO] Task started: CheckM
[2024-01-24 14:13:00,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/checkm_input GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/checkm_result
[2024-01-24 14:13:21,020] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:21,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:21,041] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:21,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:21,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/markers.fasta)
[2024-01-24 14:13:21,042] [INFO] Task started: Blastn
[2024-01-24 14:13:21,042] [INFO] Running command: blastn -query GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/markers.fasta -db /var/lib/cwl/stg23e283e7-a5a2-43e2-9f18-2191604e09f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:21,821] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:21,825] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:21,825] [INFO] Target genome list was writen to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:21,835] [INFO] Task started: fastANI
[2024-01-24 14:13:21,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1a7d32-de08-484c-b44a-0a64e6f936cc/GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna.gz --refList GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/target_genomes_gtdb.txt --output GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:28,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:28,093] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:28,093] [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_000518165.1	s__Bartonella elizabethae	99.9472	620	634	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	conclusive
GCF_003606325.2	s__Bartonella kosoyi	94.5869	608	634	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_003606345.3	s__Bartonella krasnovii	91.5471	590	634	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	90.9231	546	634	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_000196435.1	s__Bartonella tribocorum	90.3989	587	634	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_002777915.1	s__Bartonella tribocorum_A	90.1353	573	634	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_018155095.1	s__Bartonella queenslandensis_B	89.9091	559	634	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_000312585.1	s__Bartonella queenslandensis_A	89.3346	556	634	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	89.2826	539	634	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_902150025.1	s__Bartonella massiliensis	89.1348	563	634	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	82.7509	495	634	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_000312545.1	s__Bartonella senegalensis	82.1903	473	634	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 14:13:28,099] [INFO] GTDB search result was written to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:28,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:28,104] [INFO] DFAST_QC result json was written to GCF_902825135.1_Bartonella_elizabethae_ATCC_49927_genomic.fna/dqc_result.json
[2024-01-24 14:13:28,105] [INFO] DFAST_QC completed!
[2024-01-24 14:13:28,105] [INFO] Total running time: 0h0m41s