[2023-06-26 21:00:28,560] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:00:28,562] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:00:28,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference
[2023-06-26 21:00:30,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:00:30,197] [INFO] Task started: Prodigal
[2023-06-26 21:00:30,198] [INFO] Running command: gunzip -c /var/lib/cwl/stg5026d7f6-eb39-4dc1-82f3-3cfb3459496b/GCA_026004095.1_ASM2600409v1_genomic.fna.gz | prodigal -d GCA_026004095.1_ASM2600409v1_genomic.fna/cds.fna -a GCA_026004095.1_ASM2600409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:00:38,045] [INFO] Task succeeded: Prodigal
[2023-06-26 21:00:38,046] [INFO] Task started: HMMsearch
[2023-06-26 21:00:38,047] [INFO] Running command: hmmsearch --tblout GCA_026004095.1_ASM2600409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/reference_markers.hmm GCA_026004095.1_ASM2600409v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:00:38,230] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:00:38,231] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5026d7f6-eb39-4dc1-82f3-3cfb3459496b/GCA_026004095.1_ASM2600409v1_genomic.fna.gz]
[2023-06-26 21:00:38,259] [INFO] Query marker FASTA was written to GCA_026004095.1_ASM2600409v1_genomic.fna/markers.fasta
[2023-06-26 21:00:38,259] [INFO] Task started: Blastn
[2023-06-26 21:00:38,259] [INFO] Running command: blastn -query GCA_026004095.1_ASM2600409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/reference_markers.fasta -out GCA_026004095.1_ASM2600409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:00:38,841] [INFO] Task succeeded: Blastn
[2023-06-26 21:00:38,846] [INFO] Selected 7 target genomes.
[2023-06-26 21:00:38,846] [INFO] Target genome list was writen to GCA_026004095.1_ASM2600409v1_genomic.fna/target_genomes.txt
[2023-06-26 21:00:38,848] [INFO] Task started: fastANI
[2023-06-26 21:00:38,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg5026d7f6-eb39-4dc1-82f3-3cfb3459496b/GCA_026004095.1_ASM2600409v1_genomic.fna.gz --refList GCA_026004095.1_ASM2600409v1_genomic.fna/target_genomes.txt --output GCA_026004095.1_ASM2600409v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:00:44,012] [INFO] Task succeeded: fastANI
[2023-06-26 21:00:44,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:00:44,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:00:44,019] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 21:00:44,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 21:00:44,020] [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	94.5494	744	904	95	below_threshold
Meiothermus ruber	strain=DSM 1279	GCA_000376665.1	277	277	type	True	94.5154	740	904	95	below_threshold
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	84.4129	624	904	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	82.5754	597	904	95	below_threshold
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	82.5509	582	904	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	79.3975	415	904	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	79.3394	378	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:00:44,022] [INFO] DFAST Taxonomy check result was written to GCA_026004095.1_ASM2600409v1_genomic.fna/tc_result.tsv
[2023-06-26 21:00:44,022] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:00:44,022] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:00:44,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/checkm_data
[2023-06-26 21:00:44,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:00:44,056] [INFO] Task started: CheckM
[2023-06-26 21:00:44,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026004095.1_ASM2600409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026004095.1_ASM2600409v1_genomic.fna/checkm_input GCA_026004095.1_ASM2600409v1_genomic.fna/checkm_result
[2023-06-26 21:01:10,740] [INFO] Task succeeded: CheckM
[2023-06-26 21:01:10,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 21:01:10,774] [INFO] ===== Completeness check finished =====
[2023-06-26 21:01:10,774] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:01:10,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026004095.1_ASM2600409v1_genomic.fna/markers.fasta)
[2023-06-26 21:01:10,775] [INFO] Task started: Blastn
[2023-06-26 21:01:10,775] [INFO] Running command: blastn -query GCA_026004095.1_ASM2600409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe926f92-ffcd-44f8-9bf9-88042c62cc58/dqc_reference/reference_markers_gtdb.fasta -out GCA_026004095.1_ASM2600409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:01:11,561] [INFO] Task succeeded: Blastn
[2023-06-26 21:01:11,565] [INFO] Selected 7 target genomes.
[2023-06-26 21:01:11,565] [INFO] Target genome list was writen to GCA_026004095.1_ASM2600409v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:01:11,570] [INFO] Task started: fastANI
[2023-06-26 21:01:11,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg5026d7f6-eb39-4dc1-82f3-3cfb3459496b/GCA_026004095.1_ASM2600409v1_genomic.fna.gz --refList GCA_026004095.1_ASM2600409v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026004095.1_ASM2600409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:01:16,925] [INFO] Task succeeded: fastANI
[2023-06-26 21:01:16,933] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 21:01:16,933] [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_000024425.1	s__Meiothermus ruber	94.5668	743	904	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	-
GCA_000482765.1	s__Meiothermus taiwanensis	92.6566	700	904	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.41	99.02	0.97	0.95	5	-
GCA_011327565.1	s__Meiothermus ruber_A	91.7547	656	904	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	84.4242	624	904	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	82.5957	596	904	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_017497985.1	s__Meiothermus sp017497985	82.3501	593	904	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226535.1	s__Meiothermus_B sp003226535	78.8816	313	904	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus_B	95.0	99.73	99.73	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-26 21:01:16,935] [INFO] GTDB search result was written to GCA_026004095.1_ASM2600409v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:01:16,936] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:01:16,939] [INFO] DFAST_QC result json was written to GCA_026004095.1_ASM2600409v1_genomic.fna/dqc_result.json
[2023-06-26 21:01:16,939] [INFO] DFAST_QC completed!
[2023-06-26 21:01:16,939] [INFO] Total running time: 0h0m48s