[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,763] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cff039c-8264-4ff4-a6df-804e6cfd6279/GCF_014201625.1_ASM1420162v1_genomic.fna.gz | prodigal -d GCF_014201625.1_ASM1420162v1_genomic.fna/cds.fna -a GCF_014201625.1_ASM1420162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:16,712] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:16,713] [INFO] Task started: HMMsearch
[2024-01-24 11:05:16,713] [INFO] Running command: hmmsearch --tblout GCF_014201625.1_ASM1420162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/reference_markers.hmm GCF_014201625.1_ASM1420162v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:17,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:17,010] [INFO] Found 6/6 markers.
[2024-01-24 11:05:17,045] [INFO] Query marker FASTA was written to GCF_014201625.1_ASM1420162v1_genomic.fna/markers.fasta
[2024-01-24 11:05:17,046] [INFO] Task started: Blastn
[2024-01-24 11:05:17,046] [INFO] Running command: blastn -query GCF_014201625.1_ASM1420162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/reference_markers.fasta -out GCF_014201625.1_ASM1420162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:17,787] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:17,795] [INFO] Selected 12 target genomes.
[2024-01-24 11:05:17,796] [INFO] Target genome list was writen to GCF_014201625.1_ASM1420162v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:17,805] [INFO] Task started: fastANI
[2024-01-24 11:05:17,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cff039c-8264-4ff4-a6df-804e6cfd6279/GCF_014201625.1_ASM1420162v1_genomic.fna.gz --refList GCF_014201625.1_ASM1420162v1_genomic.fna/target_genomes.txt --output GCF_014201625.1_ASM1420162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:28,746] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:28,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:28,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:28,753] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:28,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:28,754] [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=DSM 12027	GCA_014201625.1	57497	57497	type	True	100.0	1393	1398	95	conclusive
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	99.9936	1392	1398	95	conclusive
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	87.3762	994	1398	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	86.4881	989	1398	95	below_threshold
Deinococcus frigens	strain=DSM 12807	GCA_000701425.1	249403	249403	type	True	86.268	919	1398	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	86.1604	1091	1398	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	86.1277	1092	1398	95	below_threshold
Deinococcus aquiradiocola	strain=JCM 14371	GCA_014646915.1	393059	393059	type	True	77.7328	454	1398	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	75.4749	50	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:28,756] [INFO] DFAST Taxonomy check result was written to GCF_014201625.1_ASM1420162v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:28,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:28,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:28,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/checkm_data
[2024-01-24 11:05:28,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:28,813] [INFO] Task started: CheckM
[2024-01-24 11:05:28,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201625.1_ASM1420162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201625.1_ASM1420162v1_genomic.fna/checkm_input GCF_014201625.1_ASM1420162v1_genomic.fna/checkm_result
[2024-01-24 11:06:03,020] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:03,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:03,033] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:03,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:03,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201625.1_ASM1420162v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:03,033] [INFO] Task started: Blastn
[2024-01-24 11:06:03,033] [INFO] Running command: blastn -query GCF_014201625.1_ASM1420162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0a1630-5764-4579-aeb7-2d41d4365e1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201625.1_ASM1420162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:04,023] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:04,025] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:04,026] [INFO] Target genome list was writen to GCF_014201625.1_ASM1420162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:04,041] [INFO] Task started: fastANI
[2024-01-24 11:06:04,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cff039c-8264-4ff4-a6df-804e6cfd6279/GCF_014201625.1_ASM1420162v1_genomic.fna.gz --refList GCF_014201625.1_ASM1420162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201625.1_ASM1420162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:13,204] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,210] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:13,210] [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	99.9936	1392	1398	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	87.3979	991	1398	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	86.601	1034	1398	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	86.4933	989	1398	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	86.1604	1091	1398	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	86.0563	1007	1398	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	75.4749	50	1398	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,211] [INFO] GTDB search result was written to GCF_014201625.1_ASM1420162v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:13,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:13,214] [INFO] DFAST_QC result json was written to GCF_014201625.1_ASM1420162v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:13,214] [INFO] DFAST_QC completed!
[2024-01-24 11:06:13,214] [INFO] Total running time: 0h1m9s