[2024-01-24 12:09:05,568] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference
[2024-01-24 12:09:06,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,795] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a4e6e98-afab-40ff-8c81-c7f5cfe1d582/GCF_024622505.1_ASM2462250v1_genomic.fna.gz | prodigal -d GCF_024622505.1_ASM2462250v1_genomic.fna/cds.fna -a GCF_024622505.1_ASM2462250v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:12,832] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:12,833] [INFO] Task started: HMMsearch
[2024-01-24 12:09:12,833] [INFO] Running command: hmmsearch --tblout GCF_024622505.1_ASM2462250v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/reference_markers.hmm GCF_024622505.1_ASM2462250v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:13,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:13,092] [INFO] Found 6/6 markers.
[2024-01-24 12:09:13,121] [INFO] Query marker FASTA was written to GCF_024622505.1_ASM2462250v1_genomic.fna/markers.fasta
[2024-01-24 12:09:13,122] [INFO] Task started: Blastn
[2024-01-24 12:09:13,122] [INFO] Running command: blastn -query GCF_024622505.1_ASM2462250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/reference_markers.fasta -out GCF_024622505.1_ASM2462250v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:13,709] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:13,713] [INFO] Selected 21 target genomes.
[2024-01-24 12:09:13,713] [INFO] Target genome list was writen to GCF_024622505.1_ASM2462250v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:13,722] [INFO] Task started: fastANI
[2024-01-24 12:09:13,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a4e6e98-afab-40ff-8c81-c7f5cfe1d582/GCF_024622505.1_ASM2462250v1_genomic.fna.gz --refList GCF_024622505.1_ASM2462250v1_genomic.fna/target_genomes.txt --output GCF_024622505.1_ASM2462250v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:24,655] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:24,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:24,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:24,664] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:24,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:24,664] [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
Irregularibacter muris	strain=DSM 28593	GCA_024622505.1	1796619	1796619	type	True	100.0	1014	1017	95	conclusive
Garciella nitratireducens	strain=DSM 15102	GCA_900167305.1	218205	218205	type	True	77.1318	86	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:24,666] [INFO] DFAST Taxonomy check result was written to GCF_024622505.1_ASM2462250v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:24,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:24,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:24,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/checkm_data
[2024-01-24 12:09:24,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:24,703] [INFO] Task started: CheckM
[2024-01-24 12:09:24,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622505.1_ASM2462250v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622505.1_ASM2462250v1_genomic.fna/checkm_input GCF_024622505.1_ASM2462250v1_genomic.fna/checkm_result
[2024-01-24 12:09:48,725] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:48,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:48,748] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:48,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:48,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622505.1_ASM2462250v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:48,749] [INFO] Task started: Blastn
[2024-01-24 12:09:48,749] [INFO] Running command: blastn -query GCF_024622505.1_ASM2462250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf77c240-c3b6-4fdf-a609-09134ad36b40/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622505.1_ASM2462250v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:49,535] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:49,540] [INFO] Selected 28 target genomes.
[2024-01-24 12:09:49,540] [INFO] Target genome list was writen to GCF_024622505.1_ASM2462250v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:49,560] [INFO] Task started: fastANI
[2024-01-24 12:09:49,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a4e6e98-afab-40ff-8c81-c7f5cfe1d582/GCF_024622505.1_ASM2462250v1_genomic.fna.gz --refList GCF_024622505.1_ASM2462250v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622505.1_ASM2462250v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:02,688] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:02,692] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:10:02,693] [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_900167305.1	s__Garciella nitratireducens	77.115	85	1017	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Garciellaceae;g__Garciella	95.0	99.29	99.29	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:02,695] [INFO] GTDB search result was written to GCF_024622505.1_ASM2462250v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:02,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:02,698] [INFO] DFAST_QC result json was written to GCF_024622505.1_ASM2462250v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:02,699] [INFO] DFAST_QC completed!
[2024-01-24 12:10:02,699] [INFO] Total running time: 0h0m57s