[2024-01-24 13:49:41,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference
[2024-01-24 13:49:42,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,340] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,340] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbffa5a1-e7b5-41bf-99eb-50a9bb0f7253/GCF_014522205.1_ASM1452220v1_genomic.fna.gz | prodigal -d GCF_014522205.1_ASM1452220v1_genomic.fna/cds.fna -a GCF_014522205.1_ASM1452220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,702] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,703] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,703] [INFO] Running command: hmmsearch --tblout GCF_014522205.1_ASM1452220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/reference_markers.hmm GCF_014522205.1_ASM1452220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,914] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,940] [INFO] Query marker FASTA was written to GCF_014522205.1_ASM1452220v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,941] [INFO] Task started: Blastn
[2024-01-24 13:49:49,941] [INFO] Running command: blastn -query GCF_014522205.1_ASM1452220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/reference_markers.fasta -out GCF_014522205.1_ASM1452220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,671] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:50,671] [INFO] Target genome list was writen to GCF_014522205.1_ASM1452220v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,688] [INFO] Task started: fastANI
[2024-01-24 13:49:50,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbffa5a1-e7b5-41bf-99eb-50a9bb0f7253/GCF_014522205.1_ASM1452220v1_genomic.fna.gz --refList GCF_014522205.1_ASM1452220v1_genomic.fna/target_genomes.txt --output GCF_014522205.1_ASM1452220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,409] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:01,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:01,409] [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
Corynebacterium poyangense	strain=4H37-19	GCA_014522205.1	2684405	2684405	type	True	100.0	871	872	95	conclusive
Corynebacterium spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	77.2763	65	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,412] [INFO] DFAST Taxonomy check result was written to GCF_014522205.1_ASM1452220v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/checkm_data
[2024-01-24 13:50:01,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,441] [INFO] Task started: CheckM
[2024-01-24 13:50:01,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014522205.1_ASM1452220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014522205.1_ASM1452220v1_genomic.fna/checkm_input GCF_014522205.1_ASM1452220v1_genomic.fna/checkm_result
[2024-01-24 13:50:29,019] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:29,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:29,037] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:29,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:29,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014522205.1_ASM1452220v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:29,038] [INFO] Task started: Blastn
[2024-01-24 13:50:29,038] [INFO] Running command: blastn -query GCF_014522205.1_ASM1452220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f78b22f-5852-4814-b813-c6bdfe37c406/dqc_reference/reference_markers_gtdb.fasta -out GCF_014522205.1_ASM1452220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:29,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:30,000] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:30,000] [INFO] Target genome list was writen to GCF_014522205.1_ASM1452220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:30,046] [INFO] Task started: fastANI
[2024-01-24 13:50:30,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbffa5a1-e7b5-41bf-99eb-50a9bb0f7253/GCF_014522205.1_ASM1452220v1_genomic.fna.gz --refList GCF_014522205.1_ASM1452220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014522205.1_ASM1452220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:40,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:40,906] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:40,907] [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_014522205.1	s__Corynebacterium sp014522205	100.0	870	872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000478175.1	s__Corynebacterium sp000478175	78.8204	51	872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_900113445.1	s__Corynebacterium spheniscorum	77.2352	64	872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:40,912] [INFO] GTDB search result was written to GCF_014522205.1_ASM1452220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:40,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:40,915] [INFO] DFAST_QC result json was written to GCF_014522205.1_ASM1452220v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:40,915] [INFO] DFAST_QC completed!
[2024-01-24 13:50:40,915] [INFO] Total running time: 0h0m60s