[2024-01-24 10:48:09,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg91455084-32ba-4e2e-b5de-808d98cdbe8f/GCF_006335125.1_ASM633512v1_genomic.fna.gz | prodigal -d GCF_006335125.1_ASM633512v1_genomic.fna/cds.fna -a GCF_006335125.1_ASM633512v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:36,375] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:36,376] [INFO] Task started: HMMsearch
[2024-01-24 10:48:36,376] [INFO] Running command: hmmsearch --tblout GCF_006335125.1_ASM633512v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/reference_markers.hmm GCF_006335125.1_ASM633512v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:36,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:36,677] [INFO] Found 6/6 markers.
[2024-01-24 10:48:36,719] [INFO] Query marker FASTA was written to GCF_006335125.1_ASM633512v1_genomic.fna/markers.fasta
[2024-01-24 10:48:36,720] [INFO] Task started: Blastn
[2024-01-24 10:48:36,720] [INFO] Running command: blastn -query GCF_006335125.1_ASM633512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/reference_markers.fasta -out GCF_006335125.1_ASM633512v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:37,427] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:37,433] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:37,434] [INFO] Target genome list was writen to GCF_006335125.1_ASM633512v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:37,449] [INFO] Task started: fastANI
[2024-01-24 10:48:37,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg91455084-32ba-4e2e-b5de-808d98cdbe8f/GCF_006335125.1_ASM633512v1_genomic.fna.gz --refList GCF_006335125.1_ASM633512v1_genomic.fna/target_genomes.txt --output GCF_006335125.1_ASM633512v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:48,360] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:48,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:48,378] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:48,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:48,379] [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
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	100.0	1397	1399	95	conclusive
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	99.9935	1373	1399	95	conclusive
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	87.3995	992	1399	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	86.4501	985	1399	95	below_threshold
Deinococcus frigens	strain=DSM 12807	GCA_000701425.1	249403	249403	type	True	86.3244	920	1399	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	86.2321	1073	1399	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	86.1898	1084	1399	95	below_threshold
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	77.7609	449	1399	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	75.9492	52	1399	95	below_threshold
Thermus filiformis	strain=ATCC 43280	GCA_000771745.2	276	276	type	True	75.7507	50	1399	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	75.7187	52	1399	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	75.7156	52	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,381] [INFO] DFAST Taxonomy check result was written to GCF_006335125.1_ASM633512v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:48,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:48,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:48,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/checkm_data
[2024-01-24 10:48:48,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:48,442] [INFO] Task started: CheckM
[2024-01-24 10:48:48,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006335125.1_ASM633512v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006335125.1_ASM633512v1_genomic.fna/checkm_input GCF_006335125.1_ASM633512v1_genomic.fna/checkm_result
[2024-01-24 10:49:32,094] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:32,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:32,119] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:32,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:32,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006335125.1_ASM633512v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:32,120] [INFO] Task started: Blastn
[2024-01-24 10:49:32,120] [INFO] Running command: blastn -query GCF_006335125.1_ASM633512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ee46022-8782-4b0b-9bfc-f6ef48826469/dqc_reference/reference_markers_gtdb.fasta -out GCF_006335125.1_ASM633512v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:33,413] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:33,417] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:33,417] [INFO] Target genome list was writen to GCF_006335125.1_ASM633512v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:33,424] [INFO] Task started: fastANI
[2024-01-24 10:49:33,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg91455084-32ba-4e2e-b5de-808d98cdbe8f/GCF_006335125.1_ASM633512v1_genomic.fna.gz --refList GCF_006335125.1_ASM633512v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006335125.1_ASM633512v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:42,718] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:42,733] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:42,733] [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_006335125.1	s__Deinococcus radiopugnans	100.0	1397	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	conclusive
GCF_014647055.1	s__Deinococcus aerolatus	87.4187	990	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	86.6579	1028	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701405.1	s__Deinococcus marmoris	86.4382	986	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201875.1	s__Deinococcus humi	86.1792	1085	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009017495.1	s__Deinococcus sp009017495	86.1537	999	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744885.1	s__Thermus amyloliquefaciens	75.9492	52	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771745.2	s__Thermus_A filiformis	75.7507	50	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091545.1	s__Thermus thermophilus	75.7156	52	1399	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:42,736] [INFO] GTDB search result was written to GCF_006335125.1_ASM633512v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:42,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:42,740] [INFO] DFAST_QC result json was written to GCF_006335125.1_ASM633512v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:42,740] [INFO] DFAST_QC completed!
[2024-01-24 10:49:42,740] [INFO] Total running time: 0h1m34s