[2024-01-24 12:37:09,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference
[2024-01-24 12:37:10,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,756] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,756] [INFO] Running command: gunzip -c /var/lib/cwl/stgc882fd45-5314-48ee-9ccb-2daeac8258f0/GCF_004307015.1_ASM430701v1_genomic.fna.gz | prodigal -d GCF_004307015.1_ASM430701v1_genomic.fna/cds.fna -a GCF_004307015.1_ASM430701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:22,648] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:22,648] [INFO] Task started: HMMsearch
[2024-01-24 12:37:22,648] [INFO] Running command: hmmsearch --tblout GCF_004307015.1_ASM430701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/reference_markers.hmm GCF_004307015.1_ASM430701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:22,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:22,875] [INFO] Found 6/6 markers.
[2024-01-24 12:37:22,897] [INFO] Query marker FASTA was written to GCF_004307015.1_ASM430701v1_genomic.fna/markers.fasta
[2024-01-24 12:37:22,897] [INFO] Task started: Blastn
[2024-01-24 12:37:22,897] [INFO] Running command: blastn -query GCF_004307015.1_ASM430701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/reference_markers.fasta -out GCF_004307015.1_ASM430701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:23,526] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:23,530] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:23,531] [INFO] Target genome list was writen to GCF_004307015.1_ASM430701v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:23,539] [INFO] Task started: fastANI
[2024-01-24 12:37:23,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgc882fd45-5314-48ee-9ccb-2daeac8258f0/GCF_004307015.1_ASM430701v1_genomic.fna.gz --refList GCF_004307015.1_ASM430701v1_genomic.fna/target_genomes.txt --output GCF_004307015.1_ASM430701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:32,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:32,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:32,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:32,288] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:32,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:32,289] [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 thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	100.0	726	726	95	conclusive
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	87.8402	572	726	95	below_threshold
Thermus tengchongensis	strain=YIM 77924	GCA_021462405.1	1214928	1214928	type	True	87.6502	579	726	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	86.8094	561	726	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	86.4786	574	726	95	below_threshold
Thermus caldilimi	strain=YIM 78456	GCA_004684245.1	2483360	2483360	type	True	86.4631	571	726	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	86.2971	579	726	95	below_threshold
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	86.2715	586	726	95	below_threshold
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	85.4294	563	726	95	below_threshold
Thermus brevis	strain=SYSU G05001	GCA_019430925.1	2862456	2862456	type	True	85.2195	551	726	95	below_threshold
Thermus antranikianii	strain=DSM 12462	GCA_000423905.1	88190	88190	type	True	84.9572	553	726	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	84.9078	538	726	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	84.7747	541	726	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	84.566	520	726	95	below_threshold
Thermus caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	84.485	550	726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:32,291] [INFO] DFAST Taxonomy check result was written to GCF_004307015.1_ASM430701v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:32,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:32,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:32,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/checkm_data
[2024-01-24 12:37:32,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:32,317] [INFO] Task started: CheckM
[2024-01-24 12:37:32,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004307015.1_ASM430701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004307015.1_ASM430701v1_genomic.fna/checkm_input GCF_004307015.1_ASM430701v1_genomic.fna/checkm_result
[2024-01-24 12:38:07,327] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:07,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:07,351] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:07,351] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:07,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004307015.1_ASM430701v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:07,352] [INFO] Task started: Blastn
[2024-01-24 12:38:07,352] [INFO] Running command: blastn -query GCF_004307015.1_ASM430701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d16c259-c197-4691-9b68-c7d29e0a67e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004307015.1_ASM430701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:08,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:08,292] [INFO] Selected 15 target genomes.
[2024-01-24 12:38:08,293] [INFO] Target genome list was writen to GCF_004307015.1_ASM430701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:08,309] [INFO] Task started: fastANI
[2024-01-24 12:38:08,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgc882fd45-5314-48ee-9ccb-2daeac8258f0/GCF_004307015.1_ASM430701v1_genomic.fna.gz --refList GCF_004307015.1_ASM430701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004307015.1_ASM430701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:17,370] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:17,385] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:17,385] [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_004307015.1	s__Thermus thermamylovorans	100.0	726	726	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_000745065.1	s__Thermus caliditerrae	88.0057	562	726	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	87.6512	604	726	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	86.7904	562	726	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	86.4823	574	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684245.1	s__Thermus caldilimi	86.4419	572	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236585.1	s__Thermus sp000236585	86.2789	563	726	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	86.2585	587	726	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	85.5542	550	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647535.1	s__Thermus composti	85.4962	546	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426945.1	s__Thermus sediminis	85.4306	549	726	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	85.4042	564	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.02	97.96	0.92	0.92	3	-
GCF_001880325.1	s__Thermus brockianus	84.8767	562	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001535545.1	s__Thermus parvatiensis	84.5152	522	726	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	-
GCF_003336745.1	s__Thermus caldifontis	84.4865	549	726	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 12:38:17,388] [INFO] GTDB search result was written to GCF_004307015.1_ASM430701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:17,389] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:17,393] [INFO] DFAST_QC result json was written to GCF_004307015.1_ASM430701v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:17,393] [INFO] DFAST_QC completed!
[2024-01-24 12:38:17,393] [INFO] Total running time: 0h1m8s