[2024-01-24 13:17:13,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference
[2024-01-24 13:17:15,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,042] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cc5f20c-233a-4825-9b33-2488add1e22c/GCF_000485845.1_RicGra1.0_genomic.fna.gz | prodigal -d GCF_000485845.1_RicGra1.0_genomic.fna/cds.fna -a GCF_000485845.1_RicGra1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:17,082] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:17,082] [INFO] Task started: HMMsearch
[2024-01-24 13:17:17,082] [INFO] Running command: hmmsearch --tblout GCF_000485845.1_RicGra1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/reference_markers.hmm GCF_000485845.1_RicGra1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:17,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:17,317] [INFO] Found 6/6 markers.
[2024-01-24 13:17:17,338] [INFO] Query marker FASTA was written to GCF_000485845.1_RicGra1.0_genomic.fna/markers.fasta
[2024-01-24 13:17:17,339] [INFO] Task started: Blastn
[2024-01-24 13:17:17,339] [INFO] Running command: blastn -query GCF_000485845.1_RicGra1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/reference_markers.fasta -out GCF_000485845.1_RicGra1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:18,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:18,014] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:18,015] [INFO] Target genome list was writen to GCF_000485845.1_RicGra1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:17:18,045] [INFO] Task started: fastANI
[2024-01-24 13:17:18,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc5f20c-233a-4825-9b33-2488add1e22c/GCF_000485845.1_RicGra1.0_genomic.fna.gz --refList GCF_000485845.1_RicGra1.0_genomic.fna/target_genomes.txt --output GCF_000485845.1_RicGra1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:25,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:25,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:25,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:25,545] [INFO] Found 11 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 13:17:25,545] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:17:25,545] [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 gravesii	strain=BWI-1	GCA_000485845.1	354585	354585	type	True	100.0	429	432	95	inconclusive
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	97.5334	401	432	95	inconclusive
Rickettsia japonica	strain=YH	GCA_000302635.2	35790	35790	suspected-type	True	97.3529	391	432	95	inconclusive
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	97.3309	398	432	95	inconclusive
Rickettsia conorii subsp. heilongjiangensis	strain=054	GCA_000221205.1	226665	781	suspected-type	True	97.2469	403	432	95	inconclusive
Rickettsia sibirica	strain=246	GCA_000166935.1	35793	35793	suspected-type	True	97.191	391	432	95	inconclusive
Rickettsia conorii subsp. caspia	strain=A-167	GCA_000261325.1	302011	781	suspected-type	True	97.1439	381	432	95	inconclusive
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	97.1421	399	432	95	inconclusive
Rickettsia sibirica subsp. mongolitimonae	strain=HA-91	GCA_000247625.2	45261	35793	suspected-type	True	97.1157	384	432	95	inconclusive
Rickettsia conorii subsp. israelensis	strain=ISTT CDC1	GCA_000263815.1	45258	781	suspected-type	True	97.1009	377	432	95	inconclusive
Rickettsia rickettsii	strain=Iowa	GCA_001950995.1	783	783	suspected-type	True	96.888	397	432	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:25,547] [INFO] DFAST Taxonomy check result was written to GCF_000485845.1_RicGra1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:17:25,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:25,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:25,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/checkm_data
[2024-01-24 13:17:25,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:25,565] [INFO] Task started: CheckM
[2024-01-24 13:17:25,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000485845.1_RicGra1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000485845.1_RicGra1.0_genomic.fna/checkm_input GCF_000485845.1_RicGra1.0_genomic.fna/checkm_result
[2024-01-24 13:17:40,896] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:40,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:40,919] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:40,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:40,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000485845.1_RicGra1.0_genomic.fna/markers.fasta)
[2024-01-24 13:17:40,921] [INFO] Task started: Blastn
[2024-01-24 13:17:40,921] [INFO] Running command: blastn -query GCF_000485845.1_RicGra1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0a6a024-2f8e-46d1-99b1-fb0e194893c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000485845.1_RicGra1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:41,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:41,988] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:41,988] [INFO] Target genome list was writen to GCF_000485845.1_RicGra1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:41,998] [INFO] Task started: fastANI
[2024-01-24 13:17:41,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cc5f20c-233a-4825-9b33-2488add1e22c/GCF_000485845.1_RicGra1.0_genomic.fna.gz --refList GCF_000485845.1_RicGra1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000485845.1_RicGra1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:47,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:47,046] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:17:47,047] [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_000284075.1	s__Rickettsia rhipicephali	97.3309	398	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	97.74	97.12	0.95	0.80	15	inconclusive
GCF_001951015.1	s__Rickettsia rickettsii	96.8862	397	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	inconclusive
GCF_000751075.1	s__Rickettsia tamurae	94.2084	384	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	97.18	96.01	0.86	0.73	6	-
GCF_000255355.1	s__Rickettsia helvetica_A	93.1811	390	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.64	98.64	0.94	0.94	2	-
GCF_000825685.1	s__Rickettsia hoogstraalii	93.0644	407	432	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	92.8476	354	432	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	92.8256	395	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.1029	N/A	N/A	N/A	N/A	1	-
GCF_000273745.1	s__Rickettsia australis	92.0166	367	432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:47,049] [INFO] GTDB search result was written to GCF_000485845.1_RicGra1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:47,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:47,055] [INFO] DFAST_QC result json was written to GCF_000485845.1_RicGra1.0_genomic.fna/dqc_result.json
[2024-01-24 13:17:47,056] [INFO] DFAST_QC completed!
[2024-01-24 13:17:47,056] [INFO] Total running time: 0h0m33s