[2024-01-24 11:12:27,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference
[2024-01-24 11:12:29,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,145] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg382d4454-3bf9-4c0c-b026-37840033b886/GCF_014773435.2_ASM1477343v2_genomic.fna.gz | prodigal -d GCF_014773435.2_ASM1477343v2_genomic.fna/cds.fna -a GCF_014773435.2_ASM1477343v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:36,410] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:36,411] [INFO] Task started: HMMsearch
[2024-01-24 11:12:36,411] [INFO] Running command: hmmsearch --tblout GCF_014773435.2_ASM1477343v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/reference_markers.hmm GCF_014773435.2_ASM1477343v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:36,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:36,817] [INFO] Found 6/6 markers.
[2024-01-24 11:12:36,845] [INFO] Query marker FASTA was written to GCF_014773435.2_ASM1477343v2_genomic.fna/markers.fasta
[2024-01-24 11:12:36,845] [INFO] Task started: Blastn
[2024-01-24 11:12:36,846] [INFO] Running command: blastn -query GCF_014773435.2_ASM1477343v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/reference_markers.fasta -out GCF_014773435.2_ASM1477343v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:37,512] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:37,522] [INFO] Selected 25 target genomes.
[2024-01-24 11:12:37,523] [INFO] Target genome list was writen to GCF_014773435.2_ASM1477343v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:37,538] [INFO] Task started: fastANI
[2024-01-24 11:12:37,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg382d4454-3bf9-4c0c-b026-37840033b886/GCF_014773435.2_ASM1477343v2_genomic.fna.gz --refList GCF_014773435.2_ASM1477343v2_genomic.fna/target_genomes.txt --output GCF_014773435.2_ASM1477343v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:51,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:51,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:51,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:51,698] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:12:51,698] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 11:12:51,699] [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
--------------------------------------------------------------------------------
[2024-01-24 11:12:51,700] [INFO] DFAST Taxonomy check result was written to GCF_014773435.2_ASM1477343v2_genomic.fna/tc_result.tsv
[2024-01-24 11:12:51,701] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:51,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:51,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/checkm_data
[2024-01-24 11:12:51,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:51,737] [INFO] Task started: CheckM
[2024-01-24 11:12:51,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773435.2_ASM1477343v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773435.2_ASM1477343v2_genomic.fna/checkm_input GCF_014773435.2_ASM1477343v2_genomic.fna/checkm_result
[2024-01-24 11:13:19,388] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:19,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:19,409] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:19,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:19,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773435.2_ASM1477343v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:19,410] [INFO] Task started: Blastn
[2024-01-24 11:13:19,410] [INFO] Running command: blastn -query GCF_014773435.2_ASM1477343v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7759ff65-27dd-4241-bceb-bda618f15f47/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773435.2_ASM1477343v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:20,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:20,332] [INFO] Selected 23 target genomes.
[2024-01-24 11:13:20,333] [INFO] Target genome list was writen to GCF_014773435.2_ASM1477343v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:20,375] [INFO] Task started: fastANI
[2024-01-24 11:13:20,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg382d4454-3bf9-4c0c-b026-37840033b886/GCF_014773435.2_ASM1477343v2_genomic.fna.gz --refList GCF_014773435.2_ASM1477343v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014773435.2_ASM1477343v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:34,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:34,913] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:34,913] [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_014773435.2	s__IB182353 sp014773435	100.0	1056	1057	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__IB182353	95.0	99.11	99.11	0.95	0.95	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:13:34,914] [INFO] GTDB search result was written to GCF_014773435.2_ASM1477343v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:34,915] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:34,917] [INFO] DFAST_QC result json was written to GCF_014773435.2_ASM1477343v2_genomic.fna/dqc_result.json
[2024-01-24 11:13:34,917] [INFO] DFAST_QC completed!
[2024-01-24 11:13:34,917] [INFO] Total running time: 0h1m7s