[2024-01-24 13:01:26,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,031] [INFO] DQC Reference Directory: /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference
[2024-01-24 13:01:27,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,439] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,440] [INFO] Running command: gunzip -c /var/lib/cwl/stgabc0dce7-1636-4dfe-882d-02b713ae611e/GCF_000302635.2_ASM30263v2_genomic.fna.gz | prodigal -d GCF_000302635.2_ASM30263v2_genomic.fna/cds.fna -a GCF_000302635.2_ASM30263v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:29,461] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:29,462] [INFO] Task started: HMMsearch
[2024-01-24 13:01:29,462] [INFO] Running command: hmmsearch --tblout GCF_000302635.2_ASM30263v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/reference_markers.hmm GCF_000302635.2_ASM30263v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:29,678] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:29,679] [INFO] Found 6/6 markers.
[2024-01-24 13:01:29,697] [INFO] Query marker FASTA was written to GCF_000302635.2_ASM30263v2_genomic.fna/markers.fasta
[2024-01-24 13:01:29,697] [INFO] Task started: Blastn
[2024-01-24 13:01:29,697] [INFO] Running command: blastn -query GCF_000302635.2_ASM30263v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/reference_markers.fasta -out GCF_000302635.2_ASM30263v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:30,360] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:30,363] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:30,364] [INFO] Target genome list was writen to GCF_000302635.2_ASM30263v2_genomic.fna/target_genomes.txt
[2024-01-24 13:01:30,393] [INFO] Task started: fastANI
[2024-01-24 13:01:30,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc0dce7-1636-4dfe-882d-02b713ae611e/GCF_000302635.2_ASM30263v2_genomic.fna.gz --refList GCF_000302635.2_ASM30263v2_genomic.fna/target_genomes.txt --output GCF_000302635.2_ASM30263v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:37,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:37,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:37,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:37,399] [INFO] Found 9 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:01:37,399] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:01:37,399] [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 japonica	strain=YH	GCA_000302635.2	35790	35790	suspected-type	True	99.9998	419	419	95	inconclusive
Rickettsia japonica	strain=YH	GCA_000283595.1	35790	35790	suspected-type	True	99.9851	417	419	95	inconclusive
Rickettsia conorii subsp. heilongjiangensis	strain=054	GCA_000221205.1	226665	781	suspected-type	True	99.1912	418	419	95	inconclusive
Rickettsia conorii	strain=Malish 7	GCA_000007025.1	781	781	suspected-type	True	97.7017	408	419	95	inconclusive
Rickettsia conorii subsp. caspia	strain=A-167	GCA_000261325.1	302011	781	suspected-type	True	97.6599	394	419	95	inconclusive
Rickettsia sibirica	strain=246	GCA_000166935.1	35793	35793	suspected-type	True	97.6427	407	419	95	inconclusive
Rickettsia sibirica subsp. mongolitimonae	strain=HA-91	GCA_000247625.2	45261	35793	suspected-type	True	97.5581	401	419	95	inconclusive
Rickettsia conorii subsp. israelensis	strain=ISTT CDC1	GCA_000263815.1	45258	781	suspected-type	True	97.5543	394	419	95	inconclusive
Rickettsia rhipicephali	strain=3-7-female6-CWPP	GCA_000284075.1	33992	33992	type	True	97.1967	404	419	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:01:37,404] [INFO] DFAST Taxonomy check result was written to GCF_000302635.2_ASM30263v2_genomic.fna/tc_result.tsv
[2024-01-24 13:01:37,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:37,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:37,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/checkm_data
[2024-01-24 13:01:37,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:37,435] [INFO] Task started: CheckM
[2024-01-24 13:01:37,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000302635.2_ASM30263v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000302635.2_ASM30263v2_genomic.fna/checkm_input GCF_000302635.2_ASM30263v2_genomic.fna/checkm_result
[2024-01-24 13:01:52,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:52,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:52,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:52,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:52,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000302635.2_ASM30263v2_genomic.fna/markers.fasta)
[2024-01-24 13:01:52,120] [INFO] Task started: Blastn
[2024-01-24 13:01:52,120] [INFO] Running command: blastn -query GCF_000302635.2_ASM30263v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ca749a-c83a-4a6e-943f-e490bf0c557b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000302635.2_ASM30263v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:53,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:53,193] [INFO] Selected 9 target genomes.
[2024-01-24 13:01:53,193] [INFO] Target genome list was writen to GCF_000302635.2_ASM30263v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:53,201] [INFO] Task started: fastANI
[2024-01-24 13:01:53,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc0dce7-1636-4dfe-882d-02b713ae611e/GCF_000302635.2_ASM30263v2_genomic.fna.gz --refList GCF_000302635.2_ASM30263v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000302635.2_ASM30263v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:58,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:58,695] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:01:58,696] [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_001951015.1	s__Rickettsia rickettsii	97.4891	404	419	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_000284075.1	s__Rickettsia rhipicephali	97.1967	404	419	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_000751075.1	s__Rickettsia tamurae	94.2003	383	419	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	93.3254	387	419	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	93.3024	396	419	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	92.9043	353	419	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	92.814	397	419	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Rickettsia	95.8797	98.88	96.13	0.96	0.93	5	-
GCF_016743795.1	s__Rickettsia tillamookensis	92.7477	394	419	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	92.0831	366	419	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 13:01:58,698] [INFO] GTDB search result was written to GCF_000302635.2_ASM30263v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:58,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:58,709] [INFO] DFAST_QC result json was written to GCF_000302635.2_ASM30263v2_genomic.fna/dqc_result.json
[2024-01-24 13:01:58,710] [INFO] DFAST_QC completed!
[2024-01-24 13:01:58,710] [INFO] Total running time: 0h0m33s