[2024-01-24 15:32:05,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,770] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference
[2024-01-24 15:32:07,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:07,025] [INFO] Task started: Prodigal
[2024-01-24 15:32:07,025] [INFO] Running command: gunzip -c /var/lib/cwl/stgd43eca70-8db6-460b-8e00-95bcad31ec4b/GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna.gz | prodigal -d GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/cds.fna -a GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:09,270] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:09,270] [INFO] Task started: HMMsearch
[2024-01-24 15:32:09,271] [INFO] Running command: hmmsearch --tblout GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/reference_markers.hmm GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:09,487] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:09,489] [INFO] Found 6/6 markers.
[2024-01-24 15:32:09,511] [INFO] Query marker FASTA was written to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/markers.fasta
[2024-01-24 15:32:09,512] [INFO] Task started: Blastn
[2024-01-24 15:32:09,512] [INFO] Running command: blastn -query GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/reference_markers.fasta -out GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:10,162] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:10,165] [INFO] Selected 18 target genomes.
[2024-01-24 15:32:10,166] [INFO] Target genome list was writen to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:10,173] [INFO] Task started: fastANI
[2024-01-24 15:32:10,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43eca70-8db6-460b-8e00-95bcad31ec4b/GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna.gz --refList GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/target_genomes.txt --output GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:20,329] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:20,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:20,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:20,341] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:32:20,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:20,342] [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
Rickettsia tamurae	strain=AT-1	GCA_000751075.1	334545	334545	type	True	100.0	473	473	95	conclusive
Rickettsia tamurae subsp. buchneri	strain=ISO7	GCA_000696365.2	1462938	334545	type	True	96.5184	338	473	95	conclusive
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	94.7648	419	473	95	below_threshold
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	94.4671	391	473	95	below_threshold
Rickettsia japonica	strain=YH	GCA_000302635.2	35790	35790	suspected-type	True	94.2439	379	473	95	below_threshold
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	94.2198	381	473	95	below_threshold
Rickettsia gravesii	strain=BWI-1	GCA_000485845.1	354585	354585	type	True	94.2049	394	473	95	below_threshold
Rickettsia sibirica	strain=246	GCA_000166935.1	35793	35793	suspected-type	True	94.1123	382	473	95	below_threshold
Rickettsia conorii subsp. israelensis	strain=ISTT CDC1	GCA_000263815.1	45258	781	suspected-type	True	94.1122	374	473	95	below_threshold
Rickettsia conorii subsp. caspia	strain=A-167	GCA_000261325.1	302011	781	suspected-type	True	94.0938	375	473	95	below_threshold
Rickettsia hoogstraalii	strain=Croatica	GCA_000825685.1	467174	467174	type	True	93.7578	410	473	95	below_threshold
Rickettsia tillamookensis	strain=Tillamook 23	GCA_016743795.1	2761623	2761623	type	True	93.4819	399	473	95	below_threshold
Rickettsia asembonensis	strain=NMRCii	GCA_000828125.2	1068590	1068590	type	True	93.4648	359	473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:20,343] [INFO] DFAST Taxonomy check result was written to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:20,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:20,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:20,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/checkm_data
[2024-01-24 15:32:20,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:20,366] [INFO] Task started: CheckM
[2024-01-24 15:32:20,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/checkm_input GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/checkm_result
[2024-01-24 15:32:34,901] [INFO] Task succeeded: CheckM
[2024-01-24 15:32:34,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:32:34,920] [INFO] ===== Completeness check finished =====
[2024-01-24 15:32:34,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:32:34,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/markers.fasta)
[2024-01-24 15:32:34,921] [INFO] Task started: Blastn
[2024-01-24 15:32:34,921] [INFO] Running command: blastn -query GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6db566-3ee7-40a2-bcc7-dfa14e787e9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:35,942] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:35,947] [INFO] Selected 7 target genomes.
[2024-01-24 15:32:35,947] [INFO] Target genome list was writen to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:32:35,967] [INFO] Task started: fastANI
[2024-01-24 15:32:35,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgd43eca70-8db6-460b-8e00-95bcad31ec4b/GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna.gz --refList GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/target_genomes_gtdb.txt --output GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:32:42,145] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:42,155] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:32:42,155] [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_000751075.1	s__Rickettsia tamurae	100.0	473	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	97.18	96.01	0.86	0.73	6	conclusive
GCF_000284075.1	s__Rickettsia rhipicephali	94.4671	391	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	97.74	97.12	0.95	0.80	15	-
GCF_000255355.1	s__Rickettsia helvetica_A	94.1832	411	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.64	98.64	0.94	0.94	2	-
GCF_001951015.1	s__Rickettsia rickettsii	93.9871	390	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	-
GCF_000825685.1	s__Rickettsia hoogstraalii	93.7578	410	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8684	99.00	99.00	0.94	0.94	2	-
GCF_000828125.2	s__Rickettsia asembonensis	93.5058	358	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_016743795.1	s__Rickettsia tillamookensis	93.4918	398	473	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.1029	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:32:42,157] [INFO] GTDB search result was written to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:32:42,158] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:32:42,162] [INFO] DFAST_QC result json was written to GCF_000751075.1_Rickettsia_tamurae_AT-1_genomic.fna/dqc_result.json
[2024-01-24 15:32:42,162] [INFO] DFAST_QC completed!
[2024-01-24 15:32:42,162] [INFO] Total running time: 0h0m36s