[2024-01-24 13:25:31,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference
[2024-01-24 13:25:32,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,484] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg16efecb1-e29b-426f-a9bf-820f4af2cdf2/GCF_000008045.1_ASM804v1_genomic.fna.gz | prodigal -d GCF_000008045.1_ASM804v1_genomic.fna/cds.fna -a GCF_000008045.1_ASM804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:34,208] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:34,209] [INFO] Task started: HMMsearch
[2024-01-24 13:25:34,209] [INFO] Running command: hmmsearch --tblout GCF_000008045.1_ASM804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/reference_markers.hmm GCF_000008045.1_ASM804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:34,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:34,457] [INFO] Found 6/6 markers.
[2024-01-24 13:25:34,473] [INFO] Query marker FASTA was written to GCF_000008045.1_ASM804v1_genomic.fna/markers.fasta
[2024-01-24 13:25:34,473] [INFO] Task started: Blastn
[2024-01-24 13:25:34,474] [INFO] Running command: blastn -query GCF_000008045.1_ASM804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/reference_markers.fasta -out GCF_000008045.1_ASM804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:35,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:35,126] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:35,126] [INFO] Target genome list was writen to GCF_000008045.1_ASM804v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:35,152] [INFO] Task started: fastANI
[2024-01-24 13:25:35,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg16efecb1-e29b-426f-a9bf-820f4af2cdf2/GCF_000008045.1_ASM804v1_genomic.fna.gz --refList GCF_000008045.1_ASM804v1_genomic.fna/target_genomes.txt --output GCF_000008045.1_ASM804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:41,211] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:41,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:41,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:41,229] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:41,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:41,229] [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 typhi	strain=Wilmington	GCA_000008045.1	785	785	type	True	100.0	370	370	95	conclusive
Rickettsia prowazekii	strain=Breinl	GCA_000367405.1	782	782	type	True	93.1735	349	370	95	below_threshold
Rickettsia tamurae subsp. buchneri	strain=ISO7	GCA_000696365.2	1462938	334545	type	True	86.5403	268	370	95	below_threshold
Rickettsia tamurae	strain=AT-1	GCA_000751075.1	334545	334545	type	True	86.3024	323	370	95	below_threshold
Rickettsia sibirica subsp. mongolitimonae	strain=HA-91	GCA_000247625.2	45261	35793	suspected-type	True	86.2128	322	370	95	below_threshold
Rickettsia hoogstraalii	strain=Croatica	GCA_000825685.1	467174	467174	type	True	86.2114	339	370	95	below_threshold
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	86.1979	336	370	95	below_threshold
Rickettsia japonica	strain=YH	GCA_000302635.2	35790	35790	suspected-type	True	86.1729	332	370	95	below_threshold
Rickettsia japonica	strain=YH	GCA_000283595.1	35790	35790	suspected-type	True	86.1541	333	370	95	below_threshold
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	86.1254	334	370	95	below_threshold
Rickettsia sibirica	strain=246	GCA_000166935.1	35793	35793	suspected-type	True	86.0791	336	370	95	below_threshold
Rickettsia asembonensis	strain=NMRCii	GCA_000828125.2	1068590	1068590	type	True	85.9655	314	370	95	below_threshold
Rickettsia australis	strain=Phillips	GCA_000273745.1	787	787	type	True	85.931	326	370	95	below_threshold
Rickettsia tillamookensis	strain=Tillamook 23	GCA_016743795.1	2761623	2761623	type	True	85.8573	334	370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:41,231] [INFO] DFAST Taxonomy check result was written to GCF_000008045.1_ASM804v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:41,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:41,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:41,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/checkm_data
[2024-01-24 13:25:41,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:41,247] [INFO] Task started: CheckM
[2024-01-24 13:25:41,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000008045.1_ASM804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000008045.1_ASM804v1_genomic.fna/checkm_input GCF_000008045.1_ASM804v1_genomic.fna/checkm_result
[2024-01-24 13:25:54,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:54,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:55,000] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:55,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:55,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000008045.1_ASM804v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:55,002] [INFO] Task started: Blastn
[2024-01-24 13:25:55,002] [INFO] Running command: blastn -query GCF_000008045.1_ASM804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66476be-5d38-4446-8bdc-dda217aaa2b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000008045.1_ASM804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:55,994] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:55,998] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:55,999] [INFO] Target genome list was writen to GCF_000008045.1_ASM804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:56,007] [INFO] Task started: fastANI
[2024-01-24 13:25:56,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg16efecb1-e29b-426f-a9bf-820f4af2cdf2/GCF_000008045.1_ASM804v1_genomic.fna.gz --refList GCF_000008045.1_ASM804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000008045.1_ASM804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:59,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:59,552] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:59,553] [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_000008045.1	s__Rickettsia typhi	100.0	370	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	100.00	99.99	1.00	1.00	4	conclusive
GCF_000367405.1	s__Rickettsia prowazekii	93.1735	349	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	99.93	99.87	1.00	1.00	13	-
GCF_000751075.1	s__Rickettsia tamurae	86.3024	323	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	97.18	96.01	0.86	0.73	6	-
GCF_000284075.1	s__Rickettsia rhipicephali	86.2769	331	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	97.74	97.12	0.95	0.80	15	-
GCF_000825685.1	s__Rickettsia hoogstraalii	86.1839	340	370	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	86.1019	332	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	-
GCF_000255355.1	s__Rickettsia helvetica_A	85.9924	327	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	98.64	98.64	0.94	0.94	2	-
GCA_000012145.1	s__Rickettsia felis	85.9921	329	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	98.88	96.13	0.96	0.93	5	-
GCF_000828125.2	s__Rickettsia asembonensis	85.9655	314	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_000273745.1	s__Rickettsia australis	85.9596	325	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	99.99	99.99	1.00	1.00	2	-
GCF_016743795.1	s__Rickettsia tillamookensis	85.8573	334	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.1029	N/A	N/A	N/A	N/A	1	-
GCF_000018205.1	s__Rickettsia akari	85.5821	326	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:59,554] [INFO] GTDB search result was written to GCF_000008045.1_ASM804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:59,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:59,560] [INFO] DFAST_QC result json was written to GCF_000008045.1_ASM804v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:59,560] [INFO] DFAST_QC completed!
[2024-01-24 13:25:59,560] [INFO] Total running time: 0h0m28s