[2023-06-17 08:21:45,518] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:21:45,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:21:45,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference
[2023-06-17 08:21:46,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:21:46,806] [INFO] Task started: Prodigal
[2023-06-17 08:21:46,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e2e9b5a-6517-4e7b-bd39-48d4c7f9969a/GCA_003695925.1_ASM369592v1_genomic.fna.gz | prodigal -d GCA_003695925.1_ASM369592v1_genomic.fna/cds.fna -a GCA_003695925.1_ASM369592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:21:53,351] [INFO] Task succeeded: Prodigal
[2023-06-17 08:21:53,352] [INFO] Task started: HMMsearch
[2023-06-17 08:21:53,352] [INFO] Running command: hmmsearch --tblout GCA_003695925.1_ASM369592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/reference_markers.hmm GCA_003695925.1_ASM369592v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:21:53,587] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:21:53,588] [INFO] Found 6/6 markers.
[2023-06-17 08:21:53,617] [INFO] Query marker FASTA was written to GCA_003695925.1_ASM369592v1_genomic.fna/markers.fasta
[2023-06-17 08:21:53,618] [INFO] Task started: Blastn
[2023-06-17 08:21:53,618] [INFO] Running command: blastn -query GCA_003695925.1_ASM369592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/reference_markers.fasta -out GCA_003695925.1_ASM369592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:21:54,218] [INFO] Task succeeded: Blastn
[2023-06-17 08:21:54,222] [INFO] Selected 13 target genomes.
[2023-06-17 08:21:54,222] [INFO] Target genome list was writen to GCA_003695925.1_ASM369592v1_genomic.fna/target_genomes.txt
[2023-06-17 08:21:54,227] [INFO] Task started: fastANI
[2023-06-17 08:21:54,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e2e9b5a-6517-4e7b-bd39-48d4c7f9969a/GCA_003695925.1_ASM369592v1_genomic.fna.gz --refList GCA_003695925.1_ASM369592v1_genomic.fna/target_genomes.txt --output GCA_003695925.1_ASM369592v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:22:01,138] [INFO] Task succeeded: fastANI
[2023-06-17 08:22:01,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:22:01,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:22:01,153] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:22:01,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:22:01,154] [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_000376665.1	277	277	type	True	80.306	504	780	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	80.278	516	780	95	below_threshold
Calidithermus timidus	strain=DSM 17022	GCA_000373205.1	307124	307124	type	True	79.86	337	780	95	below_threshold
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	79.6248	438	780	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	79.5011	453	780	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	79.4454	435	780	95	below_threshold
Meiothermus rufus	strain=DSM 22234	GCA_000423425.1	604332	604332	type	True	79.1496	438	780	95	below_threshold
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	77.163	187	780	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	77.0979	202	780	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	77.0408	172	780	95	below_threshold
Thermus caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	76.8714	155	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:22:01,156] [INFO] DFAST Taxonomy check result was written to GCA_003695925.1_ASM369592v1_genomic.fna/tc_result.tsv
[2023-06-17 08:22:01,157] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:22:01,157] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:22:01,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/checkm_data
[2023-06-17 08:22:01,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:22:01,193] [INFO] Task started: CheckM
[2023-06-17 08:22:01,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003695925.1_ASM369592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003695925.1_ASM369592v1_genomic.fna/checkm_input GCA_003695925.1_ASM369592v1_genomic.fna/checkm_result
[2023-06-17 08:22:26,183] [INFO] Task succeeded: CheckM
[2023-06-17 08:22:26,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:22:26,207] [INFO] ===== Completeness check finished =====
[2023-06-17 08:22:26,207] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:22:26,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003695925.1_ASM369592v1_genomic.fna/markers.fasta)
[2023-06-17 08:22:26,208] [INFO] Task started: Blastn
[2023-06-17 08:22:26,208] [INFO] Running command: blastn -query GCA_003695925.1_ASM369592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606dd189-d0ba-4208-a2d0-cbe02380b4ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_003695925.1_ASM369592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:22:27,006] [INFO] Task succeeded: Blastn
[2023-06-17 08:22:27,011] [INFO] Selected 11 target genomes.
[2023-06-17 08:22:27,011] [INFO] Target genome list was writen to GCA_003695925.1_ASM369592v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:22:27,043] [INFO] Task started: fastANI
[2023-06-17 08:22:27,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e2e9b5a-6517-4e7b-bd39-48d4c7f9969a/GCA_003695925.1_ASM369592v1_genomic.fna.gz --refList GCA_003695925.1_ASM369592v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003695925.1_ASM369592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:22:33,455] [INFO] Task succeeded: fastANI
[2023-06-17 08:22:33,470] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:22:33,470] [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	99.8204	717	780	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	82.3071	573	780	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	80.3493	486	780	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	80.2703	516	780	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	80.1828	473	780	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	80.0152	501	780	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	79.4789	455	780	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_000620065.1	s__Meiothermus cerbereus	79.4625	433	780	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423425.1	s__Meiothermus rufus	79.1405	439	780	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	77.1215	201	780	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	76.9037	153	780	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:22:33,473] [INFO] GTDB search result was written to GCA_003695925.1_ASM369592v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:22:33,474] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:22:33,479] [INFO] DFAST_QC result json was written to GCA_003695925.1_ASM369592v1_genomic.fna/dqc_result.json
[2023-06-17 08:22:33,479] [INFO] DFAST_QC completed!
[2023-06-17 08:22:33,479] [INFO] Total running time: 0h0m48s