[2024-01-25 18:42:50,324] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference
[2024-01-25 18:42:51,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,432] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,432] [INFO] Running command: gunzip -c /var/lib/cwl/stge738b4d4-a7cd-416f-8b8b-cfdd149e2133/GCF_000376665.1_ASM37666v1_genomic.fna.gz | prodigal -d GCF_000376665.1_ASM37666v1_genomic.fna/cds.fna -a GCF_000376665.1_ASM37666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:59,508] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:59,509] [INFO] Task started: HMMsearch
[2024-01-25 18:42:59,509] [INFO] Running command: hmmsearch --tblout GCF_000376665.1_ASM37666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/reference_markers.hmm GCF_000376665.1_ASM37666v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:59,691] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:59,695] [INFO] Found 6/6 markers.
[2024-01-25 18:42:59,723] [INFO] Query marker FASTA was written to GCF_000376665.1_ASM37666v1_genomic.fna/markers.fasta
[2024-01-25 18:42:59,723] [INFO] Task started: Blastn
[2024-01-25 18:42:59,723] [INFO] Running command: blastn -query GCF_000376665.1_ASM37666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/reference_markers.fasta -out GCF_000376665.1_ASM37666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:00,270] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:00,273] [INFO] Selected 7 target genomes.
[2024-01-25 18:43:00,273] [INFO] Target genome list was writen to GCF_000376665.1_ASM37666v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:00,281] [INFO] Task started: fastANI
[2024-01-25 18:43:00,281] [INFO] Running command: fastANI --query /var/lib/cwl/stge738b4d4-a7cd-416f-8b8b-cfdd149e2133/GCF_000376665.1_ASM37666v1_genomic.fna.gz --refList GCF_000376665.1_ASM37666v1_genomic.fna/target_genomes.txt --output GCF_000376665.1_ASM37666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:06,127] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:06,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:06,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:06,133] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:43:06,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:06,134] [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	100.0	1032	1032	95	conclusive
Meiothermus ruber	strain=DSM 1279	GCA_000024425.1	277	277	type	True	99.9991	1030	1032	95	conclusive
Meiothermus cerbereus	strain=DSM 11376	GCA_000620065.1	65552	65552	type	True	84.2958	767	1032	95	below_threshold
Meiothermus hypogaeus	strain=NBRC 106114	GCA_007990975.1	884155	884155	type	True	82.5685	695	1032	95	below_threshold
Meiothermus hypogaeus	strain=DSM 23238	GCA_003574035.1	884155	884155	type	True	82.2306	704	1032	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	79.7791	489	1032	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	79.3916	444	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:06,135] [INFO] DFAST Taxonomy check result was written to GCF_000376665.1_ASM37666v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:06,135] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:06,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:06,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/checkm_data
[2024-01-25 18:43:06,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:06,170] [INFO] Task started: CheckM
[2024-01-25 18:43:06,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376665.1_ASM37666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376665.1_ASM37666v1_genomic.fna/checkm_input GCF_000376665.1_ASM37666v1_genomic.fna/checkm_result
[2024-01-25 18:43:32,068] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:32,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:32,084] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:32,084] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:32,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376665.1_ASM37666v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:32,085] [INFO] Task started: Blastn
[2024-01-25 18:43:32,085] [INFO] Running command: blastn -query GCF_000376665.1_ASM37666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg891f6a43-744b-4b1b-b24b-d4a11f37b714/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376665.1_ASM37666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:32,867] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:32,870] [INFO] Selected 7 target genomes.
[2024-01-25 18:43:32,870] [INFO] Target genome list was writen to GCF_000376665.1_ASM37666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:32,874] [INFO] Task started: fastANI
[2024-01-25 18:43:32,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge738b4d4-a7cd-416f-8b8b-cfdd149e2133/GCF_000376665.1_ASM37666v1_genomic.fna.gz --refList GCF_000376665.1_ASM37666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376665.1_ASM37666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:38,905] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:38,911] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:38,911] [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	99.999	1031	1032	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.09	97.58	0.97	0.94	5	conclusive
GCA_000482765.1	s__Meiothermus taiwanensis	91.8709	843	1032	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	91.2912	810	1032	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	84.2842	768	1032	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	82.4996	711	1032	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	82.2386	703	1032	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Meiothermus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_000430045.1	s__Calidithermus chliarophilus	79.7699	491	1032	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Calidithermus	95.0	96.07	96.07	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:38,912] [INFO] GTDB search result was written to GCF_000376665.1_ASM37666v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:38,913] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:38,915] [INFO] DFAST_QC result json was written to GCF_000376665.1_ASM37666v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:38,915] [INFO] DFAST_QC completed!
[2024-01-25 18:43:38,915] [INFO] Total running time: 0h0m49s