[2023-06-13 01:01:45,644] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:01:45,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:01:45,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference
[2023-06-13 01:01:47,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:01:47,568] [INFO] Task started: Prodigal
[2023-06-13 01:01:47,569] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd4cd240-f5e6-4908-9aaa-2836c5902233/GCA_022702935.2_ASM2270293v2_genomic.fna.gz | prodigal -d GCA_022702935.2_ASM2270293v2_genomic.fna/cds.fna -a GCA_022702935.2_ASM2270293v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:01:55,335] [INFO] Task succeeded: Prodigal
[2023-06-13 01:01:55,335] [INFO] Task started: HMMsearch
[2023-06-13 01:01:55,335] [INFO] Running command: hmmsearch --tblout GCA_022702935.2_ASM2270293v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/reference_markers.hmm GCA_022702935.2_ASM2270293v2_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:01:55,546] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:01:55,547] [INFO] Found 6/6 markers.
[2023-06-13 01:01:55,575] [INFO] Query marker FASTA was written to GCA_022702935.2_ASM2270293v2_genomic.fna/markers.fasta
[2023-06-13 01:01:55,575] [INFO] Task started: Blastn
[2023-06-13 01:01:55,575] [INFO] Running command: blastn -query GCA_022702935.2_ASM2270293v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/reference_markers.fasta -out GCA_022702935.2_ASM2270293v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:01:56,174] [INFO] Task succeeded: Blastn
[2023-06-13 01:01:56,177] [INFO] Selected 22 target genomes.
[2023-06-13 01:01:56,178] [INFO] Target genome list was writen to GCA_022702935.2_ASM2270293v2_genomic.fna/target_genomes.txt
[2023-06-13 01:01:56,183] [INFO] Task started: fastANI
[2023-06-13 01:01:56,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4cd240-f5e6-4908-9aaa-2836c5902233/GCA_022702935.2_ASM2270293v2_genomic.fna.gz --refList GCA_022702935.2_ASM2270293v2_genomic.fna/target_genomes.txt --output GCA_022702935.2_ASM2270293v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:02:07,219] [INFO] Task succeeded: fastANI
[2023-06-13 01:02:07,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:02:07,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:02:07,223] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:02:07,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:02:07,223] [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
Thermoclostridium caenicola	strain=DSM 19027	GCA_900142095.1	659425	659425	type	True	76.9065	115	989	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:02:07,225] [INFO] DFAST Taxonomy check result was written to GCA_022702935.2_ASM2270293v2_genomic.fna/tc_result.tsv
[2023-06-13 01:02:07,225] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:02:07,226] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:02:07,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/checkm_data
[2023-06-13 01:02:07,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:02:07,258] [INFO] Task started: CheckM
[2023-06-13 01:02:07,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022702935.2_ASM2270293v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022702935.2_ASM2270293v2_genomic.fna/checkm_input GCA_022702935.2_ASM2270293v2_genomic.fna/checkm_result
[2023-06-13 01:02:35,425] [INFO] Task succeeded: CheckM
[2023-06-13 01:02:35,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:02:35,442] [INFO] ===== Completeness check finished =====
[2023-06-13 01:02:35,442] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:02:35,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022702935.2_ASM2270293v2_genomic.fna/markers.fasta)
[2023-06-13 01:02:35,442] [INFO] Task started: Blastn
[2023-06-13 01:02:35,442] [INFO] Running command: blastn -query GCA_022702935.2_ASM2270293v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg96f4ad76-0e71-45de-ac17-0ef7f367e479/dqc_reference/reference_markers_gtdb.fasta -out GCA_022702935.2_ASM2270293v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:02:36,392] [INFO] Task succeeded: Blastn
[2023-06-13 01:02:36,396] [INFO] Selected 22 target genomes.
[2023-06-13 01:02:36,396] [INFO] Target genome list was writen to GCA_022702935.2_ASM2270293v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:02:36,425] [INFO] Task started: fastANI
[2023-06-13 01:02:36,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4cd240-f5e6-4908-9aaa-2836c5902233/GCA_022702935.2_ASM2270293v2_genomic.fna.gz --refList GCA_022702935.2_ASM2270293v2_genomic.fna/target_genomes_gtdb.txt --output GCA_022702935.2_ASM2270293v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:02:45,350] [INFO] Task succeeded: fastANI
[2023-06-13 01:02:45,358] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 01:02:45,359] [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
GCA_002376415.1	s__DTU059 sp002376415	99.9447	858	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012719545.1	s__DTU059 sp012719545	77.8028	133	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521705.1	s__DTU059 sp012521705	77.0664	70	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840245.1	s__DTU059 sp012840245	76.9479	88	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142095.1	s__Thermoclostridium_A caenicola	76.8857	116	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003535195.1	s__DTU059 sp003535195	76.5489	94	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520615.1	s__DTU059 sp012520615	76.5101	59	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__DTU059	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719645.1	s__Thermoclostridium_A sp012719645	76.2777	59	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-8532;g__Thermoclostridium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:02:45,361] [INFO] GTDB search result was written to GCA_022702935.2_ASM2270293v2_genomic.fna/result_gtdb.tsv
[2023-06-13 01:02:45,361] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:02:45,364] [INFO] DFAST_QC result json was written to GCA_022702935.2_ASM2270293v2_genomic.fna/dqc_result.json
[2023-06-13 01:02:45,364] [INFO] DFAST_QC completed!
[2023-06-13 01:02:45,364] [INFO] Total running time: 0h0m60s