[2024-01-24 10:48:09,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,245] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stgb01d7f5a-61a3-43f2-b514-38269842bfe3/GCF_003336745.1_ASM333674v1_genomic.fna.gz | prodigal -d GCF_003336745.1_ASM333674v1_genomic.fna/cds.fna -a GCF_003336745.1_ASM333674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:36,825] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:36,825] [INFO] Task started: HMMsearch
[2024-01-24 10:48:36,825] [INFO] Running command: hmmsearch --tblout GCF_003336745.1_ASM333674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/reference_markers.hmm GCF_003336745.1_ASM333674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:37,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:37,063] [INFO] Found 6/6 markers.
[2024-01-24 10:48:37,093] [INFO] Query marker FASTA was written to GCF_003336745.1_ASM333674v1_genomic.fna/markers.fasta
[2024-01-24 10:48:37,094] [INFO] Task started: Blastn
[2024-01-24 10:48:37,094] [INFO] Running command: blastn -query GCF_003336745.1_ASM333674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/reference_markers.fasta -out GCF_003336745.1_ASM333674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:37,658] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:37,661] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:37,662] [INFO] Target genome list was writen to GCF_003336745.1_ASM333674v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:37,665] [INFO] Task started: fastANI
[2024-01-24 10:48:37,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01d7f5a-61a3-43f2-b514-38269842bfe3/GCF_003336745.1_ASM333674v1_genomic.fna.gz --refList GCF_003336745.1_ASM333674v1_genomic.fna/target_genomes.txt --output GCF_003336745.1_ASM333674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:42,484] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:42,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:42,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:42,495] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:42,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:42,496] [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 caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	100.0	701	702	95	conclusive
Thermus tenuipuniceus	strain=YIM 76954	GCA_002964845.1	2078690	2078690	type	True	88.6121	583	702	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	88.5273	590	702	95	below_threshold
Thermus brevis	strain=SYSU G05001	GCA_019430925.1	2862456	2862456	type	True	88.5073	594	702	95	below_threshold
Thermus scotoductus	strain=DSM 8553	GCA_000381045.1	37636	37636	suspected-type	True	88.0404	514	702	95	below_threshold
Thermus antranikianii	strain=DSM 12462	GCA_000423905.1	88190	88190	type	True	87.9472	576	702	95	below_threshold
Thermus caldilimi	strain=YIM 78456	GCA_004684245.1	2483360	2483360	type	True	87.5286	615	702	95	below_threshold
Thermus tengchongensis	strain=YIM 77924	GCA_021462405.1	1214928	1214928	type	True	87.233	574	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:42,497] [INFO] DFAST Taxonomy check result was written to GCF_003336745.1_ASM333674v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:42,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:42,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:42,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/checkm_data
[2024-01-24 10:48:42,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:42,521] [INFO] Task started: CheckM
[2024-01-24 10:48:42,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336745.1_ASM333674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336745.1_ASM333674v1_genomic.fna/checkm_input GCF_003336745.1_ASM333674v1_genomic.fna/checkm_result
[2024-01-24 10:49:24,102] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:24,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:24,196] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:24,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:24,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336745.1_ASM333674v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:24,197] [INFO] Task started: Blastn
[2024-01-24 10:49:24,197] [INFO] Running command: blastn -query GCF_003336745.1_ASM333674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e7e7c0b-2f4c-4ad9-894f-b20056fc9ef8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336745.1_ASM333674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:25,221] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:25,224] [INFO] Selected 7 target genomes.
[2024-01-24 10:49:25,224] [INFO] Target genome list was writen to GCF_003336745.1_ASM333674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:25,275] [INFO] Task started: fastANI
[2024-01-24 10:49:25,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01d7f5a-61a3-43f2-b514-38269842bfe3/GCF_003336745.1_ASM333674v1_genomic.fna.gz --refList GCF_003336745.1_ASM333674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336745.1_ASM333674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:30,469] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:30,478] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:30,478] [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_003336745.1	s__Thermus caldifontis	100.0	701	702	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_002964845.1	s__Thermus tenuipuniceus	88.6121	583	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744885.1	s__Thermus amyloliquefaciens	88.5273	590	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381045.1	s__Thermus scotoductus	88.0432	515	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	97.38	95.93	0.81	0.76	44	-
GCF_000423905.1	s__Thermus antranikianii	87.9472	576	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.31	98.31	0.92	0.92	2	-
GCF_004684245.1	s__Thermus caldilimi	87.5212	616	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744175.1	s__Thermus tengchongensis	87.202	587	702	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.07	97.71	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:30,480] [INFO] GTDB search result was written to GCF_003336745.1_ASM333674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:30,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:30,484] [INFO] DFAST_QC result json was written to GCF_003336745.1_ASM333674v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:30,484] [INFO] DFAST_QC completed!
[2024-01-24 10:49:30,485] [INFO] Total running time: 0h1m21s