[2024-01-24 15:10:40,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,954] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference
[2024-01-24 15:10:42,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,338] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,338] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde95c1a-5194-4b13-a299-977475cb7100/GCF_001552415.1_ASM155241v1_genomic.fna.gz | prodigal -d GCF_001552415.1_ASM155241v1_genomic.fna/cds.fna -a GCF_001552415.1_ASM155241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,976] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,977] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,977] [INFO] Running command: hmmsearch --tblout GCF_001552415.1_ASM155241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/reference_markers.hmm GCF_001552415.1_ASM155241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:51,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:51,210] [INFO] Found 6/6 markers.
[2024-01-24 15:10:51,235] [INFO] Query marker FASTA was written to GCF_001552415.1_ASM155241v1_genomic.fna/markers.fasta
[2024-01-24 15:10:51,235] [INFO] Task started: Blastn
[2024-01-24 15:10:51,235] [INFO] Running command: blastn -query GCF_001552415.1_ASM155241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/reference_markers.fasta -out GCF_001552415.1_ASM155241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:52,497] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:52,500] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:52,500] [INFO] Target genome list was writen to GCF_001552415.1_ASM155241v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:52,506] [INFO] Task started: fastANI
[2024-01-24 15:10:52,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde95c1a-5194-4b13-a299-977475cb7100/GCF_001552415.1_ASM155241v1_genomic.fna.gz --refList GCF_001552415.1_ASM155241v1_genomic.fna/target_genomes.txt --output GCF_001552415.1_ASM155241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:58,906] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:58,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:58,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:58,919] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:58,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:58,919] [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	100.0	888	890	95	conclusive
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	87.3209	747	890	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	87.2108	744	890	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	80.3881	500	890	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	78.9841	303	890	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	78.953	294	890	95	below_threshold
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	78.8084	320	890	95	below_threshold
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	78.7534	306	890	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	78.4921	279	890	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	78.0335	228	890	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	77.9899	231	890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:58,921] [INFO] DFAST Taxonomy check result was written to GCF_001552415.1_ASM155241v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:58,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:58,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:58,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/checkm_data
[2024-01-24 15:10:58,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:58,949] [INFO] Task started: CheckM
[2024-01-24 15:10:58,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552415.1_ASM155241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552415.1_ASM155241v1_genomic.fna/checkm_input GCF_001552415.1_ASM155241v1_genomic.fna/checkm_result
[2024-01-24 15:11:30,220] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:30,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,241] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:30,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:30,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552415.1_ASM155241v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:30,243] [INFO] Task started: Blastn
[2024-01-24 15:11:30,243] [INFO] Running command: blastn -query GCF_001552415.1_ASM155241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb6f79d-5bb5-43e2-b52a-8bcba500d234/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552415.1_ASM155241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:32,033] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:32,039] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:32,039] [INFO] Target genome list was writen to GCF_001552415.1_ASM155241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:32,047] [INFO] Task started: fastANI
[2024-01-24 15:11:32,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde95c1a-5194-4b13-a299-977475cb7100/GCF_001552415.1_ASM155241v1_genomic.fna.gz --refList GCF_001552415.1_ASM155241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552415.1_ASM155241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:36,748] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:36,761] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:36,762] [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	100.0	888	890	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	91.392	613	890	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	87.9085	771	890	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	87.2281	743	890	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	84.6415	449	890	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	80.3968	500	890	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	79.0956	230	890	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 15:11:36,764] [INFO] GTDB search result was written to GCF_001552415.1_ASM155241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:36,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:36,768] [INFO] DFAST_QC result json was written to GCF_001552415.1_ASM155241v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:36,768] [INFO] DFAST_QC completed!
[2024-01-24 15:11:36,768] [INFO] Total running time: 0h0m56s