[2024-01-24 13:18:25,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:25,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:25,963] [INFO] DQC Reference Directory: /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference
[2024-01-24 13:18:27,137] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,137] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg04cc9ddb-f22e-4ffe-8af4-eaa93b839df2/GCF_000423425.1_ASM42342v1_genomic.fna.gz | prodigal -d GCF_000423425.1_ASM42342v1_genomic.fna/cds.fna -a GCF_000423425.1_ASM42342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:34,070] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:34,071] [INFO] Task started: HMMsearch
[2024-01-24 13:18:34,071] [INFO] Running command: hmmsearch --tblout GCF_000423425.1_ASM42342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/reference_markers.hmm GCF_000423425.1_ASM42342v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:34,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:34,261] [INFO] Found 6/6 markers.
[2024-01-24 13:18:34,286] [INFO] Query marker FASTA was written to GCF_000423425.1_ASM42342v1_genomic.fna/markers.fasta
[2024-01-24 13:18:34,286] [INFO] Task started: Blastn
[2024-01-24 13:18:34,286] [INFO] Running command: blastn -query GCF_000423425.1_ASM42342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/reference_markers.fasta -out GCF_000423425.1_ASM42342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:34,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:34,864] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:34,864] [INFO] Target genome list was writen to GCF_000423425.1_ASM42342v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:34,868] [INFO] Task started: fastANI
[2024-01-24 13:18:34,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg04cc9ddb-f22e-4ffe-8af4-eaa93b839df2/GCF_000423425.1_ASM42342v1_genomic.fna.gz --refList GCF_000423425.1_ASM42342v1_genomic.fna/target_genomes.txt --output GCF_000423425.1_ASM42342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:40,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:40,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:40,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:40,481] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:40,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:40,481] [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
Meiothermus rufus	strain=DSM 22234	GCA_000423425.1	604332	604332	type	True	100.0	847	854	95	conclusive
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	80.6457	558	854	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	80.5931	546	854	95	below_threshold
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	80.1587	509	854	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	80.0655	519	854	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	80.0162	520	854	95	below_threshold
Meiothermus granaticius	strain=NBRC 107808	GCA_007990995.1	863370	863370	type	True	77.6697	267	854	95	below_threshold
Meiothermus granaticius	strain=AF-68	GCA_003574355.1	863370	863370	type	True	77.632	269	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:40,483] [INFO] DFAST Taxonomy check result was written to GCF_000423425.1_ASM42342v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:40,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:40,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:40,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/checkm_data
[2024-01-24 13:18:40,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:40,512] [INFO] Task started: CheckM
[2024-01-24 13:18:40,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423425.1_ASM42342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423425.1_ASM42342v1_genomic.fna/checkm_input GCF_000423425.1_ASM42342v1_genomic.fna/checkm_result
[2024-01-24 13:19:06,180] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:06,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,196] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:06,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:06,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423425.1_ASM42342v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:06,197] [INFO] Task started: Blastn
[2024-01-24 13:19:06,197] [INFO] Running command: blastn -query GCF_000423425.1_ASM42342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccc080e0-5f59-480e-a78c-ab2479b9d036/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423425.1_ASM42342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:07,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:07,061] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:07,061] [INFO] Target genome list was writen to GCF_000423425.1_ASM42342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:07,088] [INFO] Task started: fastANI
[2024-01-24 13:19:07,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg04cc9ddb-f22e-4ffe-8af4-eaa93b839df2/GCF_000423425.1_ASM42342v1_genomic.fna.gz --refList GCF_000423425.1_ASM42342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423425.1_ASM42342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:15,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,126] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,126] [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_000423425.1	s__Meiothermus rufus	100.0	847	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000482765.1	s__Meiothermus taiwanensis	80.891	529	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.41	99.02	0.97	0.95	5	-
GCF_000024425.1	s__Meiothermus ruber	80.6646	554	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCF_003574035.1	s__Meiothermus hypogaeus	80.076	518	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_000620065.1	s__Meiothermus cerbereus	80.0105	521	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497985.1	s__Meiothermus sp017497985	79.9971	549	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351145.1	s__Meiothermus sp003351145	79.8809	484	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574085.1	s__Meiothermus luteus	79.3815	427	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.87	99.87	0.92	0.92	2	-
GCF_003574355.1	s__Meiothermus granaticius	77.6202	270	854	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.97	99.97	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,128] [INFO] GTDB search result was written to GCF_000423425.1_ASM42342v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,132] [INFO] DFAST_QC result json was written to GCF_000423425.1_ASM42342v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,132] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,132] [INFO] Total running time: 0h0m49s