[2024-01-25 17:40:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference
[2024-01-25 17:40:36,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,670] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg721be139-49cd-42f5-be71-780196a5b366/GCF_903679515.1_669_genomic.fna.gz | prodigal -d GCF_903679515.1_669_genomic.fna/cds.fna -a GCF_903679515.1_669_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:40,298] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:40,298] [INFO] Task started: HMMsearch
[2024-01-25 17:40:40,298] [INFO] Running command: hmmsearch --tblout GCF_903679515.1_669_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/reference_markers.hmm GCF_903679515.1_669_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:40,499] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:40,500] [INFO] Found 6/6 markers.
[2024-01-25 17:40:40,521] [INFO] Query marker FASTA was written to GCF_903679515.1_669_genomic.fna/markers.fasta
[2024-01-25 17:40:40,521] [INFO] Task started: Blastn
[2024-01-25 17:40:40,521] [INFO] Running command: blastn -query GCF_903679515.1_669_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/reference_markers.fasta -out GCF_903679515.1_669_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:41,123] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:41,126] [INFO] Selected 13 target genomes.
[2024-01-25 17:40:41,126] [INFO] Target genome list was writen to GCF_903679515.1_669_genomic.fna/target_genomes.txt
[2024-01-25 17:40:41,146] [INFO] Task started: fastANI
[2024-01-25 17:40:41,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg721be139-49cd-42f5-be71-780196a5b366/GCF_903679515.1_669_genomic.fna.gz --refList GCF_903679515.1_669_genomic.fna/target_genomes.txt --output GCF_903679515.1_669_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:47,946] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:47,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:47,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:47,955] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:47,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:47,955] [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 gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	100.0	593	599	95	conclusive
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	91.0178	558	599	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	90.9832	541	599	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	90.9139	539	599	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	90.8925	539	599	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	90.4236	563	599	95	below_threshold
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	90.2157	566	599	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	90.186	560	599	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	90.0666	459	599	95	below_threshold
Bartonella massiliensis	strain=OS09	GCA_902150025.1	929795	929795	type	True	89.1179	546	599	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	84.3239	486	599	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.5777	454	599	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.5474	458	599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:47,957] [INFO] DFAST Taxonomy check result was written to GCF_903679515.1_669_genomic.fna/tc_result.tsv
[2024-01-25 17:40:47,957] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:47,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:47,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/checkm_data
[2024-01-25 17:40:47,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:47,981] [INFO] Task started: CheckM
[2024-01-25 17:40:47,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903679515.1_669_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903679515.1_669_genomic.fna/checkm_input GCF_903679515.1_669_genomic.fna/checkm_result
[2024-01-25 17:41:05,042] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:05,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:05,070] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:05,070] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:05,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903679515.1_669_genomic.fna/markers.fasta)
[2024-01-25 17:41:05,071] [INFO] Task started: Blastn
[2024-01-25 17:41:05,071] [INFO] Running command: blastn -query GCF_903679515.1_669_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ddf5a09-1cd7-402b-a6a2-0c0e324a6b5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_903679515.1_669_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:06,147] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:06,151] [INFO] Selected 11 target genomes.
[2024-01-25 17:41:06,151] [INFO] Target genome list was writen to GCF_903679515.1_669_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:06,166] [INFO] Task started: fastANI
[2024-01-25 17:41:06,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg721be139-49cd-42f5-be71-780196a5b366/GCF_903679515.1_669_genomic.fna.gz --refList GCF_903679515.1_669_genomic.fna/target_genomes_gtdb.txt --output GCF_903679515.1_669_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:12,285] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:12,293] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:12,293] [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_903679515.1	s__Bartonella gabonensis	100.0	593	599	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_000518165.1	s__Bartonella elizabethae	90.8719	539	599	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	-
GCF_003606325.2	s__Bartonella kosoyi	90.4621	560	599	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	90.2334	565	599	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_003606345.3	s__Bartonella krasnovii	90.186	560	599	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_002777915.1	s__Bartonella tribocorum_A	90.0965	548	599	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	89.6052	542	599	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	89.4356	525	599	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	89.4224	513	599	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	89.1349	545	599	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_000518085.1	s__Bartonella grahamii	88.7753	524	599	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:12,296] [INFO] GTDB search result was written to GCF_903679515.1_669_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:12,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:12,300] [INFO] DFAST_QC result json was written to GCF_903679515.1_669_genomic.fna/dqc_result.json
[2024-01-25 17:41:12,300] [INFO] DFAST_QC completed!
[2024-01-25 17:41:12,301] [INFO] Total running time: 0h0m37s