[2023-06-19 03:05:41,432] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:05:41,435] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:05:41,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference
[2023-06-19 03:05:43,744] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:05:43,745] [INFO] Task started: Prodigal
[2023-06-19 03:05:43,746] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4966a1d-12f7-47fd-ab64-c2409825f421/GCA_013178175.1_ASM1317817v1_genomic.fna.gz | prodigal -d GCA_013178175.1_ASM1317817v1_genomic.fna/cds.fna -a GCA_013178175.1_ASM1317817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:05:47,377] [INFO] Task succeeded: Prodigal
[2023-06-19 03:05:47,378] [INFO] Task started: HMMsearch
[2023-06-19 03:05:47,378] [INFO] Running command: hmmsearch --tblout GCA_013178175.1_ASM1317817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/reference_markers.hmm GCA_013178175.1_ASM1317817v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:05:47,577] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:05:47,579] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd4966a1d-12f7-47fd-ab64-c2409825f421/GCA_013178175.1_ASM1317817v1_genomic.fna.gz]
[2023-06-19 03:05:47,600] [INFO] Query marker FASTA was written to GCA_013178175.1_ASM1317817v1_genomic.fna/markers.fasta
[2023-06-19 03:05:47,601] [INFO] Task started: Blastn
[2023-06-19 03:05:47,601] [INFO] Running command: blastn -query GCA_013178175.1_ASM1317817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/reference_markers.fasta -out GCA_013178175.1_ASM1317817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:05:48,164] [INFO] Task succeeded: Blastn
[2023-06-19 03:05:48,172] [INFO] Selected 1 target genomes.
[2023-06-19 03:05:48,173] [INFO] Target genome list was writen to GCA_013178175.1_ASM1317817v1_genomic.fna/target_genomes.txt
[2023-06-19 03:05:48,175] [INFO] Task started: fastANI
[2023-06-19 03:05:48,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4966a1d-12f7-47fd-ab64-c2409825f421/GCA_013178175.1_ASM1317817v1_genomic.fna.gz --refList GCA_013178175.1_ASM1317817v1_genomic.fna/target_genomes.txt --output GCA_013178175.1_ASM1317817v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:05:48,677] [INFO] Task succeeded: fastANI
[2023-06-19 03:05:48,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:05:48,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:05:48,685] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:05:48,685] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:05:48,685] [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
Methanothermobacter tenebrarum	strain=RMAS	GCA_023167465.1	680118	680118	type	True	87.4994	407	516	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:05:48,688] [INFO] DFAST Taxonomy check result was written to GCA_013178175.1_ASM1317817v1_genomic.fna/tc_result.tsv
[2023-06-19 03:05:48,689] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:05:48,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:05:48,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/checkm_data
[2023-06-19 03:05:48,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:05:48,707] [INFO] Task started: CheckM
[2023-06-19 03:05:48,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013178175.1_ASM1317817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013178175.1_ASM1317817v1_genomic.fna/checkm_input GCA_013178175.1_ASM1317817v1_genomic.fna/checkm_result
[2023-06-19 03:06:09,200] [INFO] Task succeeded: CheckM
[2023-06-19 03:06:09,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:06:09,225] [INFO] ===== Completeness check finished =====
[2023-06-19 03:06:09,225] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:06:09,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013178175.1_ASM1317817v1_genomic.fna/markers.fasta)
[2023-06-19 03:06:09,226] [INFO] Task started: Blastn
[2023-06-19 03:06:09,227] [INFO] Running command: blastn -query GCA_013178175.1_ASM1317817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb66632ba-530e-439c-a863-3af0ce0ad316/dqc_reference/reference_markers_gtdb.fasta -out GCA_013178175.1_ASM1317817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:06:09,743] [INFO] Task succeeded: Blastn
[2023-06-19 03:06:09,746] [INFO] Selected 5 target genomes.
[2023-06-19 03:06:09,746] [INFO] Target genome list was writen to GCA_013178175.1_ASM1317817v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:06:09,751] [INFO] Task started: fastANI
[2023-06-19 03:06:09,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4966a1d-12f7-47fd-ab64-c2409825f421/GCA_013178175.1_ASM1317817v1_genomic.fna.gz --refList GCA_013178175.1_ASM1317817v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013178175.1_ASM1317817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:06:11,728] [INFO] Task succeeded: fastANI
[2023-06-19 03:06:11,734] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:06:11,734] [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_003264935.1	s__Methanothermobacter_A tenebrarum	99.9488	477	516	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae_A;g__Methanothermobacter_A	95.0	99.54	99.28	0.98	0.95	4	conclusive
GCA_012840175.1	s__Methanothermobacter_A sp012840175	87.4826	396	516	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae_A;g__Methanothermobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507955.1	s__Methanothermobacter_A sp001507955	86.9326	322	516	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae_A;g__Methanothermobacter_A	95.0	99.54	99.35	0.85	0.77	3	-
GCA_003584625.1	s__Methanothermobacter_A sp003584625	86.1162	430	516	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae_A;g__Methanothermobacter_A	95.0	99.98	99.98	0.96	0.96	2	-
GCA_011370395.1	s__Methanothermobacter_A sp011370395	83.7343	322	516	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae_A;g__Methanothermobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:06:11,736] [INFO] GTDB search result was written to GCA_013178175.1_ASM1317817v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:06:11,737] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:06:11,739] [INFO] DFAST_QC result json was written to GCA_013178175.1_ASM1317817v1_genomic.fna/dqc_result.json
[2023-06-19 03:06:11,740] [INFO] DFAST_QC completed!
[2023-06-19 03:06:11,740] [INFO] Total running time: 0h0m30s