[2024-01-24 13:40:28,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b3ff67b-5b1b-4712-8631-681bf8d04642/GCF_000988235.1_ASM98823v1_genomic.fna.gz | prodigal -d GCF_000988235.1_ASM98823v1_genomic.fna/cds.fna -a GCF_000988235.1_ASM98823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:39,006] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:39,006] [INFO] Task started: HMMsearch
[2024-01-24 13:40:39,006] [INFO] Running command: hmmsearch --tblout GCF_000988235.1_ASM98823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/reference_markers.hmm GCF_000988235.1_ASM98823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:39,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:39,258] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b3ff67b-5b1b-4712-8631-681bf8d04642/GCF_000988235.1_ASM98823v1_genomic.fna.gz]
[2024-01-24 13:40:39,295] [INFO] Query marker FASTA was written to GCF_000988235.1_ASM98823v1_genomic.fna/markers.fasta
[2024-01-24 13:40:39,296] [INFO] Task started: Blastn
[2024-01-24 13:40:39,296] [INFO] Running command: blastn -query GCF_000988235.1_ASM98823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/reference_markers.fasta -out GCF_000988235.1_ASM98823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:40,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:40,443] [INFO] Selected 9 target genomes.
[2024-01-24 13:40:40,443] [INFO] Target genome list was writen to GCF_000988235.1_ASM98823v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:40,447] [INFO] Task started: fastANI
[2024-01-24 13:40:40,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b3ff67b-5b1b-4712-8631-681bf8d04642/GCF_000988235.1_ASM98823v1_genomic.fna.gz --refList GCF_000988235.1_ASM98823v1_genomic.fna/target_genomes.txt --output GCF_000988235.1_ASM98823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:45,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:45,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:45,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:45,722] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:45,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:45,722] [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 xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	99.93	832	843	95	conclusive
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	87.3366	711	843	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	87.2661	718	843	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	80.5203	494	843	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.298	281	843	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	79.2165	260	843	95	below_threshold
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	78.8675	315	843	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	78.7791	302	843	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	78.683	266	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:45,724] [INFO] DFAST Taxonomy check result was written to GCF_000988235.1_ASM98823v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:45,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:45,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:45,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/checkm_data
[2024-01-24 13:40:45,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:45,756] [INFO] Task started: CheckM
[2024-01-24 13:40:45,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000988235.1_ASM98823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000988235.1_ASM98823v1_genomic.fna/checkm_input GCF_000988235.1_ASM98823v1_genomic.fna/checkm_result
[2024-01-24 13:41:15,160] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:15,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,182] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:15,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:15,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000988235.1_ASM98823v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:15,184] [INFO] Task started: Blastn
[2024-01-24 13:41:15,184] [INFO] Running command: blastn -query GCF_000988235.1_ASM98823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd386b8-c440-46ba-b8c8-d84214a8cb5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000988235.1_ASM98823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:16,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:16,892] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:16,893] [INFO] Target genome list was writen to GCF_000988235.1_ASM98823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:16,909] [INFO] Task started: fastANI
[2024-01-24 13:41:16,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b3ff67b-5b1b-4712-8631-681bf8d04642/GCF_000988235.1_ASM98823v1_genomic.fna.gz --refList GCF_000988235.1_ASM98823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000988235.1_ASM98823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:21,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:21,579] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:21,579] [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_001552415.1	s__Corynebacterium xerosis	99.93	832	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	95.54	0.95	0.90	8	conclusive
GCA_012837295.1	s__Corynebacterium sp012837295	91.5838	586	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001056295.1	s__Corynebacterium halotolerans_A	87.9344	730	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876455.1	s__Corynebacterium freneyi	87.2641	718	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCA_012838715.1	s__Corynebacterium sp012838715	84.6828	428	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	80.5327	493	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209905.1	s__Corynebacterium sp019209905	79.1845	223	843	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,581] [INFO] GTDB search result was written to GCF_000988235.1_ASM98823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:21,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:21,588] [INFO] DFAST_QC result json was written to GCF_000988235.1_ASM98823v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:21,589] [INFO] DFAST_QC completed!
[2024-01-24 13:41:21,589] [INFO] Total running time: 0h0m53s