[2024-01-25 20:11:35,353] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:35,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:35,357] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference
[2024-01-25 20:11:36,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:36,532] [INFO] Task started: Prodigal
[2024-01-25 20:11:36,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg84602c6c-c820-4861-a32a-1abfe655d283/GCF_000367405.1_ASM36740v1_genomic.fna.gz | prodigal -d GCF_000367405.1_ASM36740v1_genomic.fna/cds.fna -a GCF_000367405.1_ASM36740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:38,030] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:38,030] [INFO] Task started: HMMsearch
[2024-01-25 20:11:38,030] [INFO] Running command: hmmsearch --tblout GCF_000367405.1_ASM36740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/reference_markers.hmm GCF_000367405.1_ASM36740v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:38,212] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:38,213] [INFO] Found 6/6 markers.
[2024-01-25 20:11:38,225] [INFO] Query marker FASTA was written to GCF_000367405.1_ASM36740v1_genomic.fna/markers.fasta
[2024-01-25 20:11:38,226] [INFO] Task started: Blastn
[2024-01-25 20:11:38,226] [INFO] Running command: blastn -query GCF_000367405.1_ASM36740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/reference_markers.fasta -out GCF_000367405.1_ASM36740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:38,791] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:38,793] [INFO] Selected 18 target genomes.
[2024-01-25 20:11:38,794] [INFO] Target genome list was writen to GCF_000367405.1_ASM36740v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:38,859] [INFO] Task started: fastANI
[2024-01-25 20:11:38,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg84602c6c-c820-4861-a32a-1abfe655d283/GCF_000367405.1_ASM36740v1_genomic.fna.gz --refList GCF_000367405.1_ASM36740v1_genomic.fna/target_genomes.txt --output GCF_000367405.1_ASM36740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:11:44,845] [INFO] Task succeeded: fastANI
[2024-01-25 20:11:44,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:11:44,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:11:44,854] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:11:44,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:11:44,854] [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 prowazekii	strain=Breinl	GCA_000367405.1	782	782	type	True	100.0	369	369	95	conclusive
Rickettsia typhi	strain=Wilmington	GCA_000008045.1	785	785	type	True	93.1129	357	369	95	below_threshold
Rickettsia tamurae subsp. buchneri	strain=ISO7	GCA_000696365.2	1462938	334545	type	True	86.77	267	369	95	below_threshold
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	86.6476	330	369	95	below_threshold
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	86.5797	325	369	95	below_threshold
Rickettsia tamurae	strain=AT-1	GCA_000751075.1	334545	334545	type	True	86.5565	326	369	95	below_threshold
Rickettsia conorii subsp. heilongjiangensis	strain=054	GCA_000221205.1	226665	781	suspected-type	True	86.4469	333	369	95	below_threshold
Rickettsia hoogstraalii	strain=Croatica	GCA_000825685.1	467174	467174	type	True	86.4304	347	369	95	below_threshold
Rickettsia rickettsii	strain=Iowa	GCA_001950995.1	783	783	suspected-type	True	86.3725	335	369	95	below_threshold
Rickettsia rickettsii	strain=Iowa	GCA_000017445.3	783	783	suspected-type	True	86.37	335	369	95	below_threshold
Rickettsia japonica	strain=YH	GCA_000302635.2	35790	35790	suspected-type	True	86.3631	336	369	95	below_threshold
Rickettsia australis	strain=Phillips	GCA_000273745.1	787	787	type	True	86.2574	325	369	95	below_threshold
Rickettsia asembonensis	strain=NMRCii	GCA_000828125.2	1068590	1068590	type	True	86.1003	320	369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:11:44,855] [INFO] DFAST Taxonomy check result was written to GCF_000367405.1_ASM36740v1_genomic.fna/tc_result.tsv
[2024-01-25 20:11:44,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:11:44,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:11:44,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/checkm_data
[2024-01-25 20:11:44,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:11:44,869] [INFO] Task started: CheckM
[2024-01-25 20:11:44,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367405.1_ASM36740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367405.1_ASM36740v1_genomic.fna/checkm_input GCF_000367405.1_ASM36740v1_genomic.fna/checkm_result
[2024-01-25 20:11:56,377] [INFO] Task succeeded: CheckM
[2024-01-25 20:11:56,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:11:56,392] [INFO] ===== Completeness check finished =====
[2024-01-25 20:11:56,392] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:11:56,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367405.1_ASM36740v1_genomic.fna/markers.fasta)
[2024-01-25 20:11:56,392] [INFO] Task started: Blastn
[2024-01-25 20:11:56,393] [INFO] Running command: blastn -query GCF_000367405.1_ASM36740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95cd998-81a4-48c5-aaa4-44daae33c90f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367405.1_ASM36740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:57,313] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:57,315] [INFO] Selected 11 target genomes.
[2024-01-25 20:11:57,316] [INFO] Target genome list was writen to GCF_000367405.1_ASM36740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:11:57,333] [INFO] Task started: fastANI
[2024-01-25 20:11:57,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg84602c6c-c820-4861-a32a-1abfe655d283/GCF_000367405.1_ASM36740v1_genomic.fna.gz --refList GCF_000367405.1_ASM36740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367405.1_ASM36740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:00,484] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:00,491] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:00,491] [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_000367405.1	s__Rickettsia prowazekii	100.0	369	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	99.93	99.87	1.00	1.00	13	conclusive
GCF_000008045.1	s__Rickettsia typhi	93.1129	357	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000284075.1	s__Rickettsia rhipicephali	86.5797	325	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	97.74	97.12	0.95	0.80	15	-
GCF_000751075.1	s__Rickettsia tamurae	86.5565	326	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	97.18	96.01	0.86	0.73	6	-
GCF_000825685.1	s__Rickettsia hoogstraalii	86.4299	347	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8684	99.00	99.00	0.94	0.94	2	-
GCF_001951015.1	s__Rickettsia rickettsii	86.3725	335	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	-
GCF_000273745.1	s__Rickettsia australis	86.2574	325	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	99.99	99.99	1.00	1.00	2	-
GCF_000255355.1	s__Rickettsia helvetica_A	86.2009	331	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.64	98.64	0.94	0.94	2	-
GCF_000828125.2	s__Rickettsia asembonensis	86.1292	319	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	N/A	N/A	N/A	N/A	1	-
GCA_000012145.1	s__Rickettsia felis	86.0962	337	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	98.88	96.13	0.96	0.93	5	-
GCF_000018205.1	s__Rickettsia akari	85.8186	327	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:00,493] [INFO] GTDB search result was written to GCF_000367405.1_ASM36740v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:00,493] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:00,496] [INFO] DFAST_QC result json was written to GCF_000367405.1_ASM36740v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:00,496] [INFO] DFAST_QC completed!
[2024-01-25 20:12:00,496] [INFO] Total running time: 0h0m25s