[2023-06-18 11:44:52,841] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:52,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:52,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference
[2023-06-18 11:44:54,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:54,211] [INFO] Task started: Prodigal
[2023-06-18 11:44:54,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da8fbd0-7f02-48b2-89cb-1c42289c6c06/GCA_014361335.1_ASM1436133v1_genomic.fna.gz | prodigal -d GCA_014361335.1_ASM1436133v1_genomic.fna/cds.fna -a GCA_014361335.1_ASM1436133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:44:57,013] [INFO] Task succeeded: Prodigal
[2023-06-18 11:44:57,013] [INFO] Task started: HMMsearch
[2023-06-18 11:44:57,013] [INFO] Running command: hmmsearch --tblout GCA_014361335.1_ASM1436133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/reference_markers.hmm GCA_014361335.1_ASM1436133v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:44:57,191] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:44:57,192] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3da8fbd0-7f02-48b2-89cb-1c42289c6c06/GCA_014361335.1_ASM1436133v1_genomic.fna.gz]
[2023-06-18 11:44:57,212] [INFO] Query marker FASTA was written to GCA_014361335.1_ASM1436133v1_genomic.fna/markers.fasta
[2023-06-18 11:44:57,213] [INFO] Task started: Blastn
[2023-06-18 11:44:57,213] [INFO] Running command: blastn -query GCA_014361335.1_ASM1436133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/reference_markers.fasta -out GCA_014361335.1_ASM1436133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:44:57,800] [INFO] Task succeeded: Blastn
[2023-06-18 11:44:57,809] [INFO] Selected 1 target genomes.
[2023-06-18 11:44:57,810] [INFO] Target genome list was writen to GCA_014361335.1_ASM1436133v1_genomic.fna/target_genomes.txt
[2023-06-18 11:44:57,811] [INFO] Task started: fastANI
[2023-06-18 11:44:57,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da8fbd0-7f02-48b2-89cb-1c42289c6c06/GCA_014361335.1_ASM1436133v1_genomic.fna.gz --refList GCA_014361335.1_ASM1436133v1_genomic.fna/target_genomes.txt --output GCA_014361335.1_ASM1436133v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:44:58,286] [INFO] Task succeeded: fastANI
[2023-06-18 11:44:58,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:44:58,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:44:58,291] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:44:58,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:44:58,291] [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	87.6305	317	355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:44:58,293] [INFO] DFAST Taxonomy check result was written to GCA_014361335.1_ASM1436133v1_genomic.fna/tc_result.tsv
[2023-06-18 11:44:58,294] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:44:58,294] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:44:58,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/checkm_data
[2023-06-18 11:44:58,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:44:58,311] [INFO] Task started: CheckM
[2023-06-18 11:44:58,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014361335.1_ASM1436133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014361335.1_ASM1436133v1_genomic.fna/checkm_input GCA_014361335.1_ASM1436133v1_genomic.fna/checkm_result
[2023-06-18 11:45:15,542] [INFO] Task succeeded: CheckM
[2023-06-18 11:45:15,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:45:15,567] [INFO] ===== Completeness check finished =====
[2023-06-18 11:45:15,568] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:45:15,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014361335.1_ASM1436133v1_genomic.fna/markers.fasta)
[2023-06-18 11:45:15,569] [INFO] Task started: Blastn
[2023-06-18 11:45:15,569] [INFO] Running command: blastn -query GCA_014361335.1_ASM1436133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d2de85-f9fa-4922-8493-bfcc89377824/dqc_reference/reference_markers_gtdb.fasta -out GCA_014361335.1_ASM1436133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:16,104] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:16,108] [INFO] Selected 5 target genomes.
[2023-06-18 11:45:16,108] [INFO] Target genome list was writen to GCA_014361335.1_ASM1436133v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:45:16,114] [INFO] Task started: fastANI
[2023-06-18 11:45:16,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da8fbd0-7f02-48b2-89cb-1c42289c6c06/GCA_014361335.1_ASM1436133v1_genomic.fna.gz --refList GCA_014361335.1_ASM1436133v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014361335.1_ASM1436133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:45:17,900] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:17,906] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:45:17,907] [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	99.391	350	355	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	87.6635	310	355	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	86.9415	266	355	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	85.3268	324	355	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	83.8932	263	355	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	-
--------------------------------------------------------------------------------
[2023-06-18 11:45:17,909] [INFO] GTDB search result was written to GCA_014361335.1_ASM1436133v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:45:17,909] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:45:17,912] [INFO] DFAST_QC result json was written to GCA_014361335.1_ASM1436133v1_genomic.fna/dqc_result.json
[2023-06-18 11:45:17,913] [INFO] DFAST_QC completed!
[2023-06-18 11:45:17,913] [INFO] Total running time: 0h0m25s