[2024-01-24 12:37:09,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,817] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference
[2024-01-24 12:37:11,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,162] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b756997-5855-4d7c-985a-d5629a2b9785/GCF_016743795.2_ASM1674379v2_genomic.fna.gz | prodigal -d GCF_016743795.2_ASM1674379v2_genomic.fna/cds.fna -a GCF_016743795.2_ASM1674379v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:13,476] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:13,477] [INFO] Task started: HMMsearch
[2024-01-24 12:37:13,477] [INFO] Running command: hmmsearch --tblout GCF_016743795.2_ASM1674379v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/reference_markers.hmm GCF_016743795.2_ASM1674379v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:13,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:13,714] [INFO] Found 6/6 markers.
[2024-01-24 12:37:13,735] [INFO] Query marker FASTA was written to GCF_016743795.2_ASM1674379v2_genomic.fna/markers.fasta
[2024-01-24 12:37:13,736] [INFO] Task started: Blastn
[2024-01-24 12:37:13,736] [INFO] Running command: blastn -query GCF_016743795.2_ASM1674379v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/reference_markers.fasta -out GCF_016743795.2_ASM1674379v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:14,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:14,380] [INFO] Selected 16 target genomes.
[2024-01-24 12:37:14,381] [INFO] Target genome list was writen to GCF_016743795.2_ASM1674379v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:14,487] [INFO] Task started: fastANI
[2024-01-24 12:37:14,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b756997-5855-4d7c-985a-d5629a2b9785/GCF_016743795.2_ASM1674379v2_genomic.fna.gz --refList GCF_016743795.2_ASM1674379v2_genomic.fna/target_genomes.txt --output GCF_016743795.2_ASM1674379v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:26,472] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:26,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:26,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:26,482] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:26,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:26,483] [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 tillamookensis	strain=Tillamook 23	GCA_016743795.1	2761623	2761623	type	True	99.9977	478	479	95	conclusive
Rickettsia asembonensis	strain=NMRCii	GCA_000828125.2	1068590	1068590	type	True	94.8851	385	479	95	below_threshold
Rickettsia hoogstraalii	strain=Croatica	GCA_000825685.1	467174	467174	type	True	94.8763	431	479	95	below_threshold
Rickettsia tamurae	strain=AT-1	GCA_000751075.1	334545	334545	type	True	93.3723	394	479	95	below_threshold
Rickettsia tamurae subsp. buchneri	strain=ISO7	GCA_000696365.2	1462938	334545	type	True	93.2372	304	479	95	below_threshold
Rickettsia australis	strain=Phillips	GCA_000273745.1	787	787	type	True	92.9188	386	479	95	below_threshold
Rickettsia conorii subsp. raoultii	strain=Khabarovsk	GCA_000940955.1	369822	781	type	True	92.6553	418	479	95	below_threshold
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	92.6336	399	479	95	below_threshold
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	92.5369	399	479	95	below_threshold
Rickettsia sibirica subsp. mongolitimonae	strain=HA-91	GCA_000247625.2	45261	35793	suspected-type	True	92.4508	391	479	95	below_threshold
Rickettsia conorii subsp. caspia	strain=A-167	GCA_000261325.1	302011	781	suspected-type	True	92.4374	390	479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:26,484] [INFO] DFAST Taxonomy check result was written to GCF_016743795.2_ASM1674379v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:26,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:26,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:26,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/checkm_data
[2024-01-24 12:37:26,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:26,511] [INFO] Task started: CheckM
[2024-01-24 12:37:26,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016743795.2_ASM1674379v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016743795.2_ASM1674379v2_genomic.fna/checkm_input GCF_016743795.2_ASM1674379v2_genomic.fna/checkm_result
[2024-01-24 12:37:41,857] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:41,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:41,879] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:41,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:41,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016743795.2_ASM1674379v2_genomic.fna/markers.fasta)
[2024-01-24 12:37:41,881] [INFO] Task started: Blastn
[2024-01-24 12:37:41,881] [INFO] Running command: blastn -query GCF_016743795.2_ASM1674379v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e546fd-9a28-4a9b-977a-41b650d52f4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016743795.2_ASM1674379v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:42,840] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:42,844] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:42,844] [INFO] Target genome list was writen to GCF_016743795.2_ASM1674379v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:42,853] [INFO] Task started: fastANI
[2024-01-24 12:37:42,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b756997-5855-4d7c-985a-d5629a2b9785/GCF_016743795.2_ASM1674379v2_genomic.fna.gz --refList GCF_016743795.2_ASM1674379v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016743795.2_ASM1674379v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:52,555] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:52,564] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:52,564] [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_016743795.1	s__Rickettsia tillamookensis	99.9977	477	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.1029	N/A	N/A	N/A	N/A	1	conclusive
GCA_000012145.1	s__Rickettsia felis	95.1066	435	479	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	94.8842	384	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_000825685.1	s__Rickettsia hoogstraalii	94.8763	431	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8684	99.00	99.00	0.94	0.94	2	-
GCF_000751075.1	s__Rickettsia tamurae	93.4035	393	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.0	97.18	96.01	0.86	0.73	6	-
GCF_000273745.1	s__Rickettsia australis	92.9188	386	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.501	99.99	99.99	1.00	1.00	2	-
GCF_000284075.1	s__Rickettsia rhipicephali	92.6336	399	479	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	92.5939	404	479	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	92.208	411	479	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	96.8762	98.06	97.35	0.98	0.95	75	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:52,566] [INFO] GTDB search result was written to GCF_016743795.2_ASM1674379v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:52,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:52,570] [INFO] DFAST_QC result json was written to GCF_016743795.2_ASM1674379v2_genomic.fna/dqc_result.json
[2024-01-24 12:37:52,570] [INFO] DFAST_QC completed!
[2024-01-24 12:37:52,570] [INFO] Total running time: 0h0m43s