[2024-01-24 13:36:32,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference
[2024-01-24 13:36:33,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,651] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg9121679f-f615-4912-8f2c-3da72de4f3ae/GCF_014876775.1_ASM1487677v1_genomic.fna.gz | prodigal -d GCF_014876775.1_ASM1487677v1_genomic.fna/cds.fna -a GCF_014876775.1_ASM1487677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:40,483] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:40,484] [INFO] Task started: HMMsearch
[2024-01-24 13:36:40,484] [INFO] Running command: hmmsearch --tblout GCF_014876775.1_ASM1487677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/reference_markers.hmm GCF_014876775.1_ASM1487677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:40,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:40,698] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9121679f-f615-4912-8f2c-3da72de4f3ae/GCF_014876775.1_ASM1487677v1_genomic.fna.gz]
[2024-01-24 13:36:40,722] [INFO] Query marker FASTA was written to GCF_014876775.1_ASM1487677v1_genomic.fna/markers.fasta
[2024-01-24 13:36:40,723] [INFO] Task started: Blastn
[2024-01-24 13:36:40,723] [INFO] Running command: blastn -query GCF_014876775.1_ASM1487677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/reference_markers.fasta -out GCF_014876775.1_ASM1487677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:41,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:41,215] [INFO] Selected 3 target genomes.
[2024-01-24 13:36:41,216] [INFO] Target genome list was writen to GCF_014876775.1_ASM1487677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:41,217] [INFO] Task started: fastANI
[2024-01-24 13:36:41,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg9121679f-f615-4912-8f2c-3da72de4f3ae/GCF_014876775.1_ASM1487677v1_genomic.fna.gz --refList GCF_014876775.1_ASM1487677v1_genomic.fna/target_genomes.txt --output GCF_014876775.1_ASM1487677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:42,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:42,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:42,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:42,395] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:42,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:42,395] [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
Infirmifilum lucidum	strain=3507LT	GCA_014876775.1	2776706	2776706	type	True	100.0	540	541	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:36:42,397] [INFO] DFAST Taxonomy check result was written to GCF_014876775.1_ASM1487677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:42,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:42,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:42,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/checkm_data
[2024-01-24 13:36:42,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:42,418] [INFO] Task started: CheckM
[2024-01-24 13:36:42,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014876775.1_ASM1487677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014876775.1_ASM1487677v1_genomic.fna/checkm_input GCF_014876775.1_ASM1487677v1_genomic.fna/checkm_result
[2024-01-24 13:37:07,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:07,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,502] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:07,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:07,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014876775.1_ASM1487677v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:07,503] [INFO] Task started: Blastn
[2024-01-24 13:37:07,503] [INFO] Running command: blastn -query GCF_014876775.1_ASM1487677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f5f27b-3ce2-4d11-8cf0-9c17990e4161/dqc_reference/reference_markers_gtdb.fasta -out GCF_014876775.1_ASM1487677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:08,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:08,003] [INFO] Selected 5 target genomes.
[2024-01-24 13:37:08,004] [INFO] Target genome list was writen to GCF_014876775.1_ASM1487677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:08,026] [INFO] Task started: fastANI
[2024-01-24 13:37:08,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg9121679f-f615-4912-8f2c-3da72de4f3ae/GCF_014876775.1_ASM1487677v1_genomic.fna.gz --refList GCF_014876775.1_ASM1487677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014876775.1_ASM1487677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:09,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:09,807] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:09,807] [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_014876775.1	s__Infirmifilum lucidum	100.0	540	541	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermofilales;f__Thermofilaceae;g__Infirmifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002855745.1	s__Infirmifilum sp002855745	77.6965	141	541	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermofilales;f__Thermofilaceae;g__Infirmifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:09,809] [INFO] GTDB search result was written to GCF_014876775.1_ASM1487677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:09,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:09,812] [INFO] DFAST_QC result json was written to GCF_014876775.1_ASM1487677v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:09,812] [INFO] DFAST_QC completed!
[2024-01-24 13:37:09,812] [INFO] Total running time: 0h0m37s