[2024-01-24 10:47:06,591] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference
[2024-01-24 10:47:12,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,818] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg60d3ad60-33eb-4af0-a702-be34287fe911/GCF_030408815.1_ASM3040881v1_genomic.fna.gz | prodigal -d GCF_030408815.1_ASM3040881v1_genomic.fna/cds.fna -a GCF_030408815.1_ASM3040881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,952] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,952] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,952] [INFO] Running command: hmmsearch --tblout GCF_030408815.1_ASM3040881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/reference_markers.hmm GCF_030408815.1_ASM3040881v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,193] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,225] [INFO] Query marker FASTA was written to GCF_030408815.1_ASM3040881v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,226] [INFO] Task started: Blastn
[2024-01-24 10:47:22,226] [INFO] Running command: blastn -query GCF_030408815.1_ASM3040881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/reference_markers.fasta -out GCF_030408815.1_ASM3040881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,891] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,894] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:22,895] [INFO] Target genome list was writen to GCF_030408815.1_ASM3040881v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,717] [INFO] Task started: fastANI
[2024-01-24 10:47:23,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d3ad60-33eb-4af0-a702-be34287fe911/GCF_030408815.1_ASM3040881v1_genomic.fna.gz --refList GCF_030408815.1_ASM3040881v1_genomic.fna/target_genomes.txt --output GCF_030408815.1_ASM3040881v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:32,976] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:32,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:32,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:32,989] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:32,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:32,989] [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 freiburgense	strain=DSM 45254	GCA_000428805.1	556548	556548	type	True	99.9726	958	986	95	conclusive
Corynebacterium hindlerae	strain=NML 93-0612	GCA_014117265.1	699041	699041	type	True	79.7141	57	986	95	below_threshold
Corynebacterium deserti	strain=GIMN1.010	GCA_001277995.1	1408191	1408191	type	True	78.5916	56	986	95	below_threshold
Corynebacterium durum	strain=DSM 45333	GCA_013410305.1	61592	61592	type	True	78.5396	86	986	95	below_threshold
Corynebacterium canis	strain=CCUG 58627	GCA_007859215.1	679663	679663	type	True	78.516	269	986	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	78.3453	62	986	95	below_threshold
Corynebacterium belfantii		GCA_900205605.1	2014537	2014537	type	True	76.7686	53	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:32,991] [INFO] DFAST Taxonomy check result was written to GCF_030408815.1_ASM3040881v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:32,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:32,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:32,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/checkm_data
[2024-01-24 10:47:32,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:33,046] [INFO] Task started: CheckM
[2024-01-24 10:47:33,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408815.1_ASM3040881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408815.1_ASM3040881v1_genomic.fna/checkm_input GCF_030408815.1_ASM3040881v1_genomic.fna/checkm_result
[2024-01-24 10:48:05,422] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:05,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,464] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:05,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:05,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408815.1_ASM3040881v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:05,466] [INFO] Task started: Blastn
[2024-01-24 10:48:05,466] [INFO] Running command: blastn -query GCF_030408815.1_ASM3040881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bbd889a-20ba-40a2-9c9d-3eb4b1e9b2e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408815.1_ASM3040881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:06,397] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:06,401] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:06,402] [INFO] Target genome list was writen to GCF_030408815.1_ASM3040881v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:06,499] [INFO] Task started: fastANI
[2024-01-24 10:48:06,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d3ad60-33eb-4af0-a702-be34287fe911/GCF_030408815.1_ASM3040881v1_genomic.fna.gz --refList GCF_030408815.1_ASM3040881v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408815.1_ASM3040881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:15,499] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:15,509] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:15,509] [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_000428805.1	s__Corynebacterium freiburgense	99.9726	958	986	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_014117265.1	s__Corynebacterium sp014117265	79.53	56	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.31	97.31	0.93	0.93	2	-
GCF_001277995.1	s__Corynebacterium deserti	79.2304	59	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734385.1	s__Corynebacterium sp009734385	78.5289	62	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859215.1	s__Corynebacterium canis	78.516	269	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410305.1	s__Corynebacterium durum	78.3652	85	986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	97.26	0.97	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:15,510] [INFO] GTDB search result was written to GCF_030408815.1_ASM3040881v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:15,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:15,514] [INFO] DFAST_QC result json was written to GCF_030408815.1_ASM3040881v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:15,514] [INFO] DFAST_QC completed!
[2024-01-24 10:48:15,514] [INFO] Total running time: 0h1m9s