[2024-01-24 15:18:19,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference
[2024-01-24 15:18:20,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,376] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg1fdaba03-2619-4d67-b99f-924f99f547c2/GCF_003574085.1_ASM357408v1_genomic.fna.gz | prodigal -d GCF_003574085.1_ASM357408v1_genomic.fna/cds.fna -a GCF_003574085.1_ASM357408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:27,636] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:27,637] [INFO] Task started: HMMsearch
[2024-01-24 15:18:27,637] [INFO] Running command: hmmsearch --tblout GCF_003574085.1_ASM357408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/reference_markers.hmm GCF_003574085.1_ASM357408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:27,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:27,878] [INFO] Found 6/6 markers.
[2024-01-24 15:18:27,905] [INFO] Query marker FASTA was written to GCF_003574085.1_ASM357408v1_genomic.fna/markers.fasta
[2024-01-24 15:18:27,905] [INFO] Task started: Blastn
[2024-01-24 15:18:27,905] [INFO] Running command: blastn -query GCF_003574085.1_ASM357408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/reference_markers.fasta -out GCF_003574085.1_ASM357408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:28,517] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:28,520] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:28,520] [INFO] Target genome list was writen to GCF_003574085.1_ASM357408v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:28,526] [INFO] Task started: fastANI
[2024-01-24 15:18:28,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fdaba03-2619-4d67-b99f-924f99f547c2/GCF_003574085.1_ASM357408v1_genomic.fna.gz --refList GCF_003574085.1_ASM357408v1_genomic.fna/target_genomes.txt --output GCF_003574085.1_ASM357408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:35,798] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:35,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:35,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:35,813] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:35,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:35,814] [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
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	80.6688	517	850	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	80.632	519	850	95	below_threshold
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	80.3597	350	850	95	below_threshold
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	79.957	439	850	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	79.7125	439	850	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	79.6455	435	850	95	below_threshold
Meiothermus rufus	strain=DSM 22234	GCA_000423425.1	604332	604332	type	True	79.3735	435	850	95	below_threshold
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	77.8142	203	850	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	77.801	182	850	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	77.4698	180	850	95	below_threshold
Thermus caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	77.1313	165	850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:35,816] [INFO] DFAST Taxonomy check result was written to GCF_003574085.1_ASM357408v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:35,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:35,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:35,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/checkm_data
[2024-01-24 15:18:35,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:35,846] [INFO] Task started: CheckM
[2024-01-24 15:18:35,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574085.1_ASM357408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574085.1_ASM357408v1_genomic.fna/checkm_input GCF_003574085.1_ASM357408v1_genomic.fna/checkm_result
[2024-01-24 15:19:03,355] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:03,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:03,400] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:03,401] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:03,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574085.1_ASM357408v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:03,402] [INFO] Task started: Blastn
[2024-01-24 15:19:03,402] [INFO] Running command: blastn -query GCF_003574085.1_ASM357408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f41d988-5218-443e-8cc5-b8b86f65e602/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574085.1_ASM357408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:04,323] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:04,326] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:04,326] [INFO] Target genome list was writen to GCF_003574085.1_ASM357408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:04,353] [INFO] Task started: fastANI
[2024-01-24 15:19:04,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fdaba03-2619-4d67-b99f-924f99f547c2/GCF_003574085.1_ASM357408v1_genomic.fna.gz --refList GCF_003574085.1_ASM357408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574085.1_ASM357408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:11,699] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:11,709] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:11,709] [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_003574085.1	s__Meiothermus luteus	100.0	839	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.87	99.87	0.92	0.92	2	conclusive
GCF_003351145.1	s__Meiothermus sp003351145	82.3051	562	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000482765.1	s__Meiothermus taiwanensis	80.863	496	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.41	99.02	0.97	0.95	5	-
GCF_000024425.1	s__Meiothermus ruber	80.6921	517	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCA_011327565.1	s__Meiothermus ruber_A	80.2182	455	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497985.1	s__Meiothermus sp017497985	80.0978	476	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620065.1	s__Meiothermus cerbereus	79.688	442	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574035.1	s__Meiothermus hypogaeus	79.6436	436	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_000423425.1	s__Meiothermus rufus	79.3655	437	850	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744885.1	s__Thermus amyloliquefaciens	77.7298	186	850	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	77.1647	163	850	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 15:19:11,711] [INFO] GTDB search result was written to GCF_003574085.1_ASM357408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:11,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:11,714] [INFO] DFAST_QC result json was written to GCF_003574085.1_ASM357408v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:11,714] [INFO] DFAST_QC completed!
[2024-01-24 15:19:11,714] [INFO] Total running time: 0h0m53s