[2024-01-24 13:28:02,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:02,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:02,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference
[2024-01-24 13:28:03,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,447] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg35e3208f-f327-45f9-a5cd-4e41d39c976b/GCF_021462525.1_ASM2146252v1_genomic.fna.gz | prodigal -d GCF_021462525.1_ASM2146252v1_genomic.fna/cds.fna -a GCF_021462525.1_ASM2146252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:16,700] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:16,701] [INFO] Task started: HMMsearch
[2024-01-24 13:28:16,701] [INFO] Running command: hmmsearch --tblout GCF_021462525.1_ASM2146252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/reference_markers.hmm GCF_021462525.1_ASM2146252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:16,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:16,895] [INFO] Found 6/6 markers.
[2024-01-24 13:28:16,922] [INFO] Query marker FASTA was written to GCF_021462525.1_ASM2146252v1_genomic.fna/markers.fasta
[2024-01-24 13:28:16,923] [INFO] Task started: Blastn
[2024-01-24 13:28:16,923] [INFO] Running command: blastn -query GCF_021462525.1_ASM2146252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/reference_markers.fasta -out GCF_021462525.1_ASM2146252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:17,561] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:17,564] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:17,564] [INFO] Target genome list was writen to GCF_021462525.1_ASM2146252v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:17,593] [INFO] Task started: fastANI
[2024-01-24 13:28:17,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg35e3208f-f327-45f9-a5cd-4e41d39c976b/GCF_021462525.1_ASM2146252v1_genomic.fna.gz --refList GCF_021462525.1_ASM2146252v1_genomic.fna/target_genomes.txt --output GCF_021462525.1_ASM2146252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:24,084] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:24,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:24,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:24,094] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:24,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:24,095] [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
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	100.0	746	750	95	conclusive
Thermus tengchongensis	strain=YIM 77924	GCA_021462405.1	1214928	1214928	type	True	93.6159	644	750	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	87.9598	607	750	95	below_threshold
Thermus thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	87.8369	575	750	95	below_threshold
Thermus tenuipuniceus	strain=YIM 76954	GCA_002964845.1	2078690	2078690	type	True	87.2373	592	750	95	below_threshold
Thermus brevis	strain=SYSU G05001	GCA_019430925.1	2862456	2862456	type	True	86.9797	599	750	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	86.6182	584	750	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	85.8379	596	750	95	below_threshold
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	85.7701	605	750	95	below_threshold
Thermus caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	85.5639	575	750	95	below_threshold
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	85.1691	577	750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:24,097] [INFO] DFAST Taxonomy check result was written to GCF_021462525.1_ASM2146252v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:24,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:24,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:24,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/checkm_data
[2024-01-24 13:28:24,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:24,125] [INFO] Task started: CheckM
[2024-01-24 13:28:24,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021462525.1_ASM2146252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021462525.1_ASM2146252v1_genomic.fna/checkm_input GCF_021462525.1_ASM2146252v1_genomic.fna/checkm_result
[2024-01-24 13:29:01,833] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:01,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,857] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:01,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:01,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021462525.1_ASM2146252v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:01,858] [INFO] Task started: Blastn
[2024-01-24 13:29:01,858] [INFO] Running command: blastn -query GCF_021462525.1_ASM2146252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg344dab76-b387-43ba-a78b-06a7f7029523/dqc_reference/reference_markers_gtdb.fasta -out GCF_021462525.1_ASM2146252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:02,677] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:02,681] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:02,682] [INFO] Target genome list was writen to GCF_021462525.1_ASM2146252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:02,693] [INFO] Task started: fastANI
[2024-01-24 13:29:02,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg35e3208f-f327-45f9-a5cd-4e41d39c976b/GCF_021462525.1_ASM2146252v1_genomic.fna.gz --refList GCF_021462525.1_ASM2146252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021462525.1_ASM2146252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:10,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:10,985] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:10,986] [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_000745065.1	s__Thermus caliditerrae	96.8019	670	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744175.1	s__Thermus tengchongensis	93.3045	635	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.07	97.71	0.89	0.87	3	-
GCF_000744885.1	s__Thermus amyloliquefaciens	87.9638	605	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004307015.1	s__Thermus thermamylovorans	87.8369	575	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376265.1	s__Thermus igniterrae	86.6351	583	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423905.1	s__Thermus antranikianii	86.4535	572	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.31	98.31	0.92	0.92	2	-
GCF_000236585.1	s__Thermus sp000236585	86.2711	595	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102145.1	s__Thermus arciformis	85.7842	605	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336745.1	s__Thermus caldifontis	85.5491	576	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311585.1	s__Thermus sp001311585	85.4994	369	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000794385.1	s__Thermus sp000794385	85.355	580	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001880325.1	s__Thermus brockianus	85.2927	569	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280255.1	s__Thermus aquaticus	85.1747	576	750	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.02	97.96	0.92	0.92	3	-
GCF_003426945.1	s__Thermus sediminis	84.6929	548	750	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 13:29:10,987] [INFO] GTDB search result was written to GCF_021462525.1_ASM2146252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:10,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:10,990] [INFO] DFAST_QC result json was written to GCF_021462525.1_ASM2146252v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:10,991] [INFO] DFAST_QC completed!
[2024-01-24 13:29:10,991] [INFO] Total running time: 0h1m9s