[2024-01-24 13:01:04,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:04,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:04,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference
[2024-01-24 13:01:06,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:06,816] [INFO] Task started: Prodigal
[2024-01-24 13:01:06,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c7024c0-d93d-4730-b981-223363230979/GCF_003606345.3_ASM360634v3_genomic.fna.gz | prodigal -d GCF_003606345.3_ASM360634v3_genomic.fna/cds.fna -a GCF_003606345.3_ASM360634v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:11,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:11,852] [INFO] Task started: HMMsearch
[2024-01-24 13:01:11,852] [INFO] Running command: hmmsearch --tblout GCF_003606345.3_ASM360634v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/reference_markers.hmm GCF_003606345.3_ASM360634v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:12,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:12,088] [INFO] Found 6/6 markers.
[2024-01-24 13:01:12,113] [INFO] Query marker FASTA was written to GCF_003606345.3_ASM360634v3_genomic.fna/markers.fasta
[2024-01-24 13:01:12,113] [INFO] Task started: Blastn
[2024-01-24 13:01:12,113] [INFO] Running command: blastn -query GCF_003606345.3_ASM360634v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/reference_markers.fasta -out GCF_003606345.3_ASM360634v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:14,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:14,158] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:14,158] [INFO] Target genome list was writen to GCF_003606345.3_ASM360634v3_genomic.fna/target_genomes.txt
[2024-01-24 13:01:14,254] [INFO] Task started: fastANI
[2024-01-24 13:01:14,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c7024c0-d93d-4730-b981-223363230979/GCF_003606345.3_ASM360634v3_genomic.fna.gz --refList GCF_003606345.3_ASM360634v3_genomic.fna/target_genomes.txt --output GCF_003606345.3_ASM360634v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:21,458] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:21,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:21,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:21,475] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:21,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:21,478] [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 krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	100.0	727	728	95	conclusive
Bartonella saheliensis	strain=077	GCA_902162175.1	1457016	1457016	type	True	93.0209	534	728	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_902825135.1	807	807	type	True	91.635	594	728	95	below_threshold
Bartonella mastomydis	strain=008	GCA_900185775.1	1820002	1820002	type	True	91.6217	617	728	95	below_threshold
Bartonella elizabethae	strain=F9251	GCA_000278315.1	807	807	type	True	91.5772	599	728	95	below_threshold
Bartonella elizabethae	strain=ATCC 49927	GCA_000518165.1	807	807	type	True	91.5345	594	728	95	below_threshold
Bartonella kosoyi	strain=Tel Aviv	GCA_003606325.3	2133959	2133959	type	True	90.6456	643	728	95	below_threshold
Bartonella gabonensis	strain=669	GCA_903679515.1	2699889	2699889	type	True	90.027	561	728	95	below_threshold
Bartonella tribocorum	strain=type strain:506 = CIP 105476	GCA_000196435.1	85701	85701	suspected-type	True	89.4071	654	728	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	83.6564	538	728	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	82.6149	479	728	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	82.2995	494	728	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	82.2063	496	728	95	below_threshold
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	82.2002	468	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:21,482] [INFO] DFAST Taxonomy check result was written to GCF_003606345.3_ASM360634v3_genomic.fna/tc_result.tsv
[2024-01-24 13:01:21,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:21,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:21,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/checkm_data
[2024-01-24 13:01:21,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:21,515] [INFO] Task started: CheckM
[2024-01-24 13:01:21,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003606345.3_ASM360634v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003606345.3_ASM360634v3_genomic.fna/checkm_input GCF_003606345.3_ASM360634v3_genomic.fna/checkm_result
[2024-01-24 13:01:44,724] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:44,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:44,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:44,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:44,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003606345.3_ASM360634v3_genomic.fna/markers.fasta)
[2024-01-24 13:01:44,750] [INFO] Task started: Blastn
[2024-01-24 13:01:44,750] [INFO] Running command: blastn -query GCF_003606345.3_ASM360634v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf745bda0-79f9-4802-8a5f-8b4f7f4d98b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003606345.3_ASM360634v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:45,819] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:45,823] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:45,823] [INFO] Target genome list was writen to GCF_003606345.3_ASM360634v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:45,832] [INFO] Task started: fastANI
[2024-01-24 13:01:45,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c7024c0-d93d-4730-b981-223363230979/GCF_003606345.3_ASM360634v3_genomic.fna.gz --refList GCF_003606345.3_ASM360634v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003606345.3_ASM360634v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:53,257] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:53,269] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:53,269] [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_003606345.3	s__Bartonella krasnovii	100.0	726	728	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	91.5349	592	728	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	90.6793	641	728	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	89.9992	562	728	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	89.4446	651	728	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	89.2962	611	728	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	88.8201	577	728	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	88.7669	562	728	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_000312585.1	s__Bartonella queenslandensis_A	88.5182	589	728	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	87.9092	594	728	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_000312525.1	s__Bartonella florencae	83.6443	539	728	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_902825145.1	s__Bartonella phoceensis	82.6229	478	728	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	82.1984	469	728	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 13:01:53,271] [INFO] GTDB search result was written to GCF_003606345.3_ASM360634v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:53,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:53,275] [INFO] DFAST_QC result json was written to GCF_003606345.3_ASM360634v3_genomic.fna/dqc_result.json
[2024-01-24 13:01:53,275] [INFO] DFAST_QC completed!
[2024-01-24 13:01:53,275] [INFO] Total running time: 0h0m49s