[2024-01-24 11:43:53,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,150] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference
[2024-01-24 11:43:54,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,382] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgad74dd8e-3010-4013-975f-a6a17458b873/GCF_014647055.1_ASM1464705v1_genomic.fna.gz | prodigal -d GCF_014647055.1_ASM1464705v1_genomic.fna/cds.fna -a GCF_014647055.1_ASM1464705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,650] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,651] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,651] [INFO] Running command: hmmsearch --tblout GCF_014647055.1_ASM1464705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/reference_markers.hmm GCF_014647055.1_ASM1464705v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,855] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,856] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,887] [INFO] Query marker FASTA was written to GCF_014647055.1_ASM1464705v1_genomic.fna/markers.fasta
[2024-01-24 11:44:05,888] [INFO] Task started: Blastn
[2024-01-24 11:44:05,888] [INFO] Running command: blastn -query GCF_014647055.1_ASM1464705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/reference_markers.fasta -out GCF_014647055.1_ASM1464705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,573] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,576] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:06,576] [INFO] Target genome list was writen to GCF_014647055.1_ASM1464705v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:06,579] [INFO] Task started: fastANI
[2024-01-24 11:44:06,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgad74dd8e-3010-4013-975f-a6a17458b873/GCF_014647055.1_ASM1464705v1_genomic.fna.gz --refList GCF_014647055.1_ASM1464705v1_genomic.fna/target_genomes.txt --output GCF_014647055.1_ASM1464705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:13,760] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:13,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:13,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:13,768] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:13,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:13,769] [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 aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	100.0	1279	1280	95	conclusive
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	87.4621	987	1280	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	87.4428	998	1280	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	85.8001	939	1280	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	84.9657	986	1280	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	84.9462	986	1280	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	83.1928	814	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:13,770] [INFO] DFAST Taxonomy check result was written to GCF_014647055.1_ASM1464705v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:13,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:13,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:13,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/checkm_data
[2024-01-24 11:44:13,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:13,811] [INFO] Task started: CheckM
[2024-01-24 11:44:13,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647055.1_ASM1464705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647055.1_ASM1464705v1_genomic.fna/checkm_input GCF_014647055.1_ASM1464705v1_genomic.fna/checkm_result
[2024-01-24 11:44:48,480] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:48,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:48,498] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:48,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:48,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647055.1_ASM1464705v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:48,499] [INFO] Task started: Blastn
[2024-01-24 11:44:48,499] [INFO] Running command: blastn -query GCF_014647055.1_ASM1464705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb72f2bb-62b9-4e9c-81be-2b54c8b2bf02/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647055.1_ASM1464705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:49,533] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:49,537] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:49,537] [INFO] Target genome list was writen to GCF_014647055.1_ASM1464705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:49,542] [INFO] Task started: fastANI
[2024-01-24 11:44:49,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgad74dd8e-3010-4013-975f-a6a17458b873/GCF_014647055.1_ASM1464705v1_genomic.fna.gz --refList GCF_014647055.1_ASM1464705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647055.1_ASM1464705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:56,969] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:56,976] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:56,977] [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_014647055.1	s__Deinococcus aerolatus	100.0	1279	1280	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006335125.1	s__Deinococcus radiopugnans	87.4563	989	1280	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_000701405.1	s__Deinococcus marmoris	85.7937	939	1280	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	85.6938	942	1280	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009017495.1	s__Deinococcus sp009017495	85.3107	921	1280	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	84.9762	985	1280	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647075.1	s__Deinococcus aerophilus	83.2192	809	1280	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:56,978] [INFO] GTDB search result was written to GCF_014647055.1_ASM1464705v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:56,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:56,982] [INFO] DFAST_QC result json was written to GCF_014647055.1_ASM1464705v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:56,982] [INFO] DFAST_QC completed!
[2024-01-24 11:44:56,982] [INFO] Total running time: 0h1m4s