[2024-01-24 12:15:04,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference
[2024-01-24 12:15:05,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,620] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f4e947a-1703-4fbb-89d8-9d265253f2cb/GCF_003606325.2_ASM360632v3_genomic.fna.gz | prodigal -d GCF_003606325.2_ASM360632v3_genomic.fna/cds.fna -a GCF_003606325.2_ASM360632v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:11,194] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:11,195] [INFO] Task started: HMMsearch
[2024-01-24 12:15:11,195] [INFO] Running command: hmmsearch --tblout GCF_003606325.2_ASM360632v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/reference_markers.hmm GCF_003606325.2_ASM360632v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:11,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:11,435] [INFO] Found 6/6 markers.
[2024-01-24 12:15:11,462] [INFO] Query marker FASTA was written to GCF_003606325.2_ASM360632v3_genomic.fna/markers.fasta
[2024-01-24 12:15:11,463] [INFO] Task started: Blastn
[2024-01-24 12:15:11,463] [INFO] Running command: blastn -query GCF_003606325.2_ASM360632v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/reference_markers.fasta -out GCF_003606325.2_ASM360632v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:12,155] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:12,159] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:12,159] [INFO] Target genome list was writen to GCF_003606325.2_ASM360632v3_genomic.fna/target_genomes.txt
[2024-01-24 12:15:12,167] [INFO] Task started: fastANI
[2024-01-24 12:15:12,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f4e947a-1703-4fbb-89d8-9d265253f2cb/GCF_003606325.2_ASM360632v3_genomic.fna.gz --refList GCF_003606325.2_ASM360632v3_genomic.fna/target_genomes.txt --output GCF_003606325.2_ASM360632v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:18,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:18,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:18,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:18,387] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:18,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:18,387] [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 kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	100.0	748	757	95	conclusive
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	94.5376	612	757	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	94.51	608	757	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	94.478	620	757	95	below_threshold
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	93.5084	681	757	95	below_threshold
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	93.0951	633	757	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	90.7746	636	757	95	below_threshold
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	90.7698	525	757	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.6263	526	757	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.6022	526	757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,391] [INFO] DFAST Taxonomy check result was written to GCF_003606325.2_ASM360632v3_genomic.fna/tc_result.tsv
[2024-01-24 12:15:18,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:18,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:18,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/checkm_data
[2024-01-24 12:15:18,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:18,425] [INFO] Task started: CheckM
[2024-01-24 12:15:18,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003606325.2_ASM360632v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003606325.2_ASM360632v3_genomic.fna/checkm_input GCF_003606325.2_ASM360632v3_genomic.fna/checkm_result
[2024-01-24 12:15:41,978] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,003] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:42,003] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:42,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003606325.2_ASM360632v3_genomic.fna/markers.fasta)
[2024-01-24 12:15:42,004] [INFO] Task started: Blastn
[2024-01-24 12:15:42,004] [INFO] Running command: blastn -query GCF_003606325.2_ASM360632v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9efa47-8d22-4591-8321-9ad15e831d0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003606325.2_ASM360632v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:43,014] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:43,020] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:43,020] [INFO] Target genome list was writen to GCF_003606325.2_ASM360632v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:43,029] [INFO] Task started: fastANI
[2024-01-24 12:15:43,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f4e947a-1703-4fbb-89d8-9d265253f2cb/GCF_003606325.2_ASM360632v3_genomic.fna.gz --refList GCF_003606325.2_ASM360632v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003606325.2_ASM360632v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:49,290] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:49,305] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:49,305] [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_003606325.2	s__Bartonella kosoyi	100.0	751	757	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	94.5296	606	757	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_000196435.1	s__Bartonella tribocorum	93.5204	684	757	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	91.1735	609	757	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	90.9314	597	757	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	90.7656	640	757	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	90.4106	557	757	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	90.292	590	757	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	90.0814	582	757	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	88.7118	605	757	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 12:15:49,306] [INFO] GTDB search result was written to GCF_003606325.2_ASM360632v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:49,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:49,310] [INFO] DFAST_QC result json was written to GCF_003606325.2_ASM360632v3_genomic.fna/dqc_result.json
[2024-01-24 12:15:49,310] [INFO] DFAST_QC completed!
[2024-01-24 12:15:49,310] [INFO] Total running time: 0h0m45s