[2024-01-24 13:40:45,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference
[2024-01-24 13:40:47,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,059] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bd56189-1f4b-41a3-8e33-07cf0b0176e1/GCF_000012385.1_ASM1238v1_genomic.fna.gz | prodigal -d GCF_000012385.1_ASM1238v1_genomic.fna/cds.fna -a GCF_000012385.1_ASM1238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,537] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,537] [INFO] Running command: hmmsearch --tblout GCF_000012385.1_ASM1238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/reference_markers.hmm GCF_000012385.1_ASM1238v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,778] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,803] [INFO] Query marker FASTA was written to GCF_000012385.1_ASM1238v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,804] [INFO] Task started: Blastn
[2024-01-24 13:40:49,804] [INFO] Running command: blastn -query GCF_000012385.1_ASM1238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/reference_markers.fasta -out GCF_000012385.1_ASM1238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,443] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:50,443] [INFO] Target genome list was writen to GCF_000012385.1_ASM1238v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,540] [INFO] Task started: fastANI
[2024-01-24 13:40:50,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd56189-1f4b-41a3-8e33-07cf0b0176e1/GCF_000012385.1_ASM1238v1_genomic.fna.gz --refList GCF_000012385.1_ASM1238v1_genomic.fna/target_genomes.txt --output GCF_000012385.1_ASM1238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,468] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,483] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:58,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:58,483] [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 subsp. buchneri	strain=ISO7	GCA_000696365.2	1462938	334545	type	True	81.3732	255	507	95	below_threshold
Rickettsia tamurae	strain=AT-1	GCA_000751075.1	334545	334545	type	True	80.9482	294	507	95	below_threshold
Rickettsia hoogstraalii	strain=Croatica	GCA_000825685.1	467174	467174	type	True	80.912	321	507	95	below_threshold
Rickettsia asembonensis	strain=NMRCii	GCA_000828125.2	1068590	1068590	type	True	80.8368	285	507	95	below_threshold
Rickettsia tillamookensis	strain=Tillamook 23	GCA_016743795.1	2761623	2761623	type	True	80.7213	307	507	95	below_threshold
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	80.5606	312	507	95	below_threshold
Rickettsia conorii subsp. caspia	strain=A-167	GCA_000261325.1	302011	781	suspected-type	True	80.3364	284	507	95	below_threshold
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	80.3296	296	507	95	below_threshold
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	80.2198	288	507	95	below_threshold
Rickettsia conorii subsp. israelensis	strain=ISTT CDC1	GCA_000263815.1	45258	781	suspected-type	True	80.2168	288	507	95	below_threshold
Rickettsia australis	strain=Phillips	GCA_000273745.1	787	787	type	True	80.2164	295	507	95	below_threshold
Rickettsia rickettsii	strain=Iowa	GCA_001950995.1	783	783	suspected-type	True	80.1874	291	507	95	below_threshold
Rickettsia rickettsii	strain=Iowa	GCA_001951015.1	783	783	suspected-type	True	80.1868	292	507	95	below_threshold
Rickettsia rickettsii	strain=Iowa	GCA_000017445.3	783	783	suspected-type	True	80.1646	294	507	95	below_threshold
Rickettsia sibirica subsp. mongolitimonae	strain=HA-91	GCA_000247625.2	45261	35793	suspected-type	True	80.1171	292	507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,485] [INFO] DFAST Taxonomy check result was written to GCF_000012385.1_ASM1238v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/checkm_data
[2024-01-24 13:40:58,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,509] [INFO] Task started: CheckM
[2024-01-24 13:40:58,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012385.1_ASM1238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012385.1_ASM1238v1_genomic.fna/checkm_input GCF_000012385.1_ASM1238v1_genomic.fna/checkm_result
[2024-01-24 13:41:13,805] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:13,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,828] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:13,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:13,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012385.1_ASM1238v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:13,829] [INFO] Task started: Blastn
[2024-01-24 13:41:13,829] [INFO] Running command: blastn -query GCF_000012385.1_ASM1238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a0f4ff9-9651-40b9-9da0-54daa8671efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012385.1_ASM1238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:14,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:14,862] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:14,863] [INFO] Target genome list was writen to GCF_000012385.1_ASM1238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:14,895] [INFO] Task started: fastANI
[2024-01-24 13:41:14,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd56189-1f4b-41a3-8e33-07cf0b0176e1/GCF_000012385.1_ASM1238v1_genomic.fna.gz --refList GCF_000012385.1_ASM1238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000012385.1_ASM1238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:21,186] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:21,203] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:21,203] [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_000012385.1	s__Rickettsia bellii	100.0	507	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	99.63	99.56	0.97	0.96	5	conclusive
GCF_002285905.1	s__Rickettsia sp002285905	94.0408	398	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	99.85	99.75	0.97	0.96	4	-
GCF_000751075.1	s__Rickettsia tamurae	80.933	295	507	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	80.9245	320	507	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	80.8793	281	507	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	80.6356	311	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.1029	N/A	N/A	N/A	N/A	1	-
GCA_000012145.1	s__Rickettsia felis	80.6055	322	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	98.88	96.13	0.96	0.93	5	-
GCF_000255355.1	s__Rickettsia helvetica_A	80.5037	310	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.64	98.64	0.94	0.94	2	-
GCF_000273745.1	s__Rickettsia australis	80.221	294	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	99.99	99.99	1.00	1.00	2	-
GCF_001951015.1	s__Rickettsia rickettsii	80.1575	293	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	-
GCF_000018205.1	s__Rickettsia akari	80.0701	274	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	N/A	N/A	N/A	N/A	1	-
GCF_000014345.1	s__Rickettsia canadensis	80.0112	259	507	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.93	98.93	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,205] [INFO] GTDB search result was written to GCF_000012385.1_ASM1238v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:21,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:21,210] [INFO] DFAST_QC result json was written to GCF_000012385.1_ASM1238v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:21,211] [INFO] DFAST_QC completed!
[2024-01-24 13:41:21,211] [INFO] Total running time: 0h0m35s