[2024-01-24 15:18:38,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference
[2024-01-24 15:18:40,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,011] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,012] [INFO] Running command: gunzip -c /var/lib/cwl/stge5fa9fb3-f99b-413a-bfd3-23519b83cb30/GCF_016728365.1_ASM1672836v1_genomic.fna.gz | prodigal -d GCF_016728365.1_ASM1672836v1_genomic.fna/cds.fna -a GCF_016728365.1_ASM1672836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,790] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,790] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,791] [INFO] Running command: hmmsearch --tblout GCF_016728365.1_ASM1672836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/reference_markers.hmm GCF_016728365.1_ASM1672836v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:48,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:48,121] [INFO] Found 6/6 markers.
[2024-01-24 15:18:48,153] [INFO] Query marker FASTA was written to GCF_016728365.1_ASM1672836v1_genomic.fna/markers.fasta
[2024-01-24 15:18:48,153] [INFO] Task started: Blastn
[2024-01-24 15:18:48,155] [INFO] Running command: blastn -query GCF_016728365.1_ASM1672836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/reference_markers.fasta -out GCF_016728365.1_ASM1672836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,301] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,307] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:49,308] [INFO] Target genome list was writen to GCF_016728365.1_ASM1672836v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,321] [INFO] Task started: fastANI
[2024-01-24 15:18:49,321] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fa9fb3-f99b-413a-bfd3-23519b83cb30/GCF_016728365.1_ASM1672836v1_genomic.fna.gz --refList GCF_016728365.1_ASM1672836v1_genomic.fna/target_genomes.txt --output GCF_016728365.1_ASM1672836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:58,733] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:58,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:58,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:58,746] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:58,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:58,746] [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 tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	100.0	817	817	95	conclusive
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	99.9966	815	817	95	conclusive
Corynebacterium accolens	strain=DSM 44278	GCA_023520795.1	38284	38284	type	True	82.098	537	817	95	below_threshold
Corynebacterium accolens	strain=ATCC 49725	GCA_000159115.1	38284	38284	type	True	81.7778	525	817	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	80.2701	347	817	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	80.1939	373	817	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	80.1043	361	817	95	below_threshold
Corynebacterium macginleyi	strain=CCUG 32361	GCA_003688935.1	38290	38290	type	True	80.0659	422	817	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.8615	324	817	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	79.7731	327	817	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	79.5532	306	817	95	below_threshold
Corynebacterium flavescens	strain=OJ8	GCA_001941465.1	28028	28028	type	True	79.4162	271	817	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	78.0642	165	817	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	77.9508	163	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:58,748] [INFO] DFAST Taxonomy check result was written to GCF_016728365.1_ASM1672836v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:58,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:58,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:58,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/checkm_data
[2024-01-24 15:18:58,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:58,778] [INFO] Task started: CheckM
[2024-01-24 15:18:58,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016728365.1_ASM1672836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016728365.1_ASM1672836v1_genomic.fna/checkm_input GCF_016728365.1_ASM1672836v1_genomic.fna/checkm_result
[2024-01-24 15:19:27,510] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:27,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:27,531] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:27,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:27,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016728365.1_ASM1672836v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:27,532] [INFO] Task started: Blastn
[2024-01-24 15:19:27,532] [INFO] Running command: blastn -query GCF_016728365.1_ASM1672836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46794e1f-989e-4655-8f99-7d9af50a8906/dqc_reference/reference_markers_gtdb.fasta -out GCF_016728365.1_ASM1672836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:28,638] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:28,642] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:28,642] [INFO] Target genome list was writen to GCF_016728365.1_ASM1672836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:28,647] [INFO] Task started: fastANI
[2024-01-24 15:19:28,647] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fa9fb3-f99b-413a-bfd3-23519b83cb30/GCF_016728365.1_ASM1672836v1_genomic.fna.gz --refList GCF_016728365.1_ASM1672836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016728365.1_ASM1672836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:32,922] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:32,933] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:32,933] [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_013408445.1	s__Corynebacterium tuberculostearicum	99.9966	815	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	conclusive
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	96.2775	711	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	95.0385	710	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCA_900539985.1	s__Corynebacterium sp900539985	94.8764	631	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.98	0.92	0.92	2	-
GCF_016127015.1	s__Corynebacterium aurimucosum_E	94.4739	716	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.91	96.45	0.92	0.89	6	-
GCF_002154655.1	s__Corynebacterium kefirresidentii	89.3095	690	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.23	95.39	0.90	0.89	9	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,935] [INFO] GTDB search result was written to GCF_016728365.1_ASM1672836v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:32,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:32,939] [INFO] DFAST_QC result json was written to GCF_016728365.1_ASM1672836v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:32,939] [INFO] DFAST_QC completed!
[2024-01-24 15:19:32,939] [INFO] Total running time: 0h0m54s