[2024-01-24 13:46:18,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,474] [INFO] DQC Reference Directory: /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference
[2024-01-24 13:46:19,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,916] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c78a25-9fc2-4485-8338-b1077cff520b/GCF_014335175.1_LK23_genomic.fna.gz | prodigal -d GCF_014335175.1_LK23_genomic.fna/cds.fna -a GCF_014335175.1_LK23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:27,847] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:27,848] [INFO] Task started: HMMsearch
[2024-01-24 13:46:27,848] [INFO] Running command: hmmsearch --tblout GCF_014335175.1_LK23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/reference_markers.hmm GCF_014335175.1_LK23_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:28,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:28,112] [INFO] Found 6/6 markers.
[2024-01-24 13:46:28,135] [INFO] Query marker FASTA was written to GCF_014335175.1_LK23_genomic.fna/markers.fasta
[2024-01-24 13:46:28,136] [INFO] Task started: Blastn
[2024-01-24 13:46:28,136] [INFO] Running command: blastn -query GCF_014335175.1_LK23_genomic.fna/markers.fasta -db /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/reference_markers.fasta -out GCF_014335175.1_LK23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:29,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:29,053] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:29,053] [INFO] Target genome list was writen to GCF_014335175.1_LK23_genomic.fna/target_genomes.txt
[2024-01-24 13:46:29,059] [INFO] Task started: fastANI
[2024-01-24 13:46:29,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c78a25-9fc2-4485-8338-b1077cff520b/GCF_014335175.1_LK23_genomic.fna.gz --refList GCF_014335175.1_LK23_genomic.fna/target_genomes.txt --output GCF_014335175.1_LK23_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:36,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:36,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:36,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:36,259] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:36,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:36,259] [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 amycolatum	strain=LK23	GCA_014335175.1	43765	43765	type	True	100.0	813	813	95	conclusive
Corynebacterium amycolatum	strain=FDAARGOS_1189	GCA_016889425.1	43765	43765	type	True	99.9958	813	813	95	conclusive
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	80.0773	407	813	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	78.7823	250	813	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	78.7166	247	813	95	below_threshold
Corynebacterium xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	78.1668	257	813	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	77.9654	150	813	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	76.165	58	813	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	75.9458	60	813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:36,261] [INFO] DFAST Taxonomy check result was written to GCF_014335175.1_LK23_genomic.fna/tc_result.tsv
[2024-01-24 13:46:36,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:36,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:36,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/checkm_data
[2024-01-24 13:46:36,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:36,297] [INFO] Task started: CheckM
[2024-01-24 13:46:36,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014335175.1_LK23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014335175.1_LK23_genomic.fna/checkm_input GCF_014335175.1_LK23_genomic.fna/checkm_result
[2024-01-24 13:47:04,795] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:04,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:04,818] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:04,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:04,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014335175.1_LK23_genomic.fna/markers.fasta)
[2024-01-24 13:47:04,819] [INFO] Task started: Blastn
[2024-01-24 13:47:04,819] [INFO] Running command: blastn -query GCF_014335175.1_LK23_genomic.fna/markers.fasta -db /var/lib/cwl/stga5798bff-59ab-4e41-99b8-dd2f9a8bf1a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014335175.1_LK23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:06,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:06,119] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:06,119] [INFO] Target genome list was writen to GCF_014335175.1_LK23_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:06,143] [INFO] Task started: fastANI
[2024-01-24 13:47:06,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c78a25-9fc2-4485-8338-b1077cff520b/GCF_014335175.1_LK23_genomic.fna.gz --refList GCF_014335175.1_LK23_genomic.fna/target_genomes_gtdb.txt --output GCF_014335175.1_LK23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:10,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:10,635] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:10,636] [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_016889425.1	s__Corynebacterium amycolatum	99.9958	813	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.33	95.20	0.94	0.89	32	conclusive
GCF_000173655.1	s__Corynebacterium amycolatum_A	94.6053	747	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.32	95.17	0.90	0.87	42	-
GCF_001054325.1	s__Corynebacterium vitaeruminis_A	92.3091	738	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274895.1	s__Corynebacterium lactis	80.0773	407	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900519355.1	s__Corynebacterium lactis_A	80.0269	440	813	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	78.7823	250	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCF_017942225.1	s__Corynebacterium sp017942225	78.1391	97	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838715.1	s__Corynebacterium sp012838715	78.0822	169	813	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 13:47:10,637] [INFO] GTDB search result was written to GCF_014335175.1_LK23_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:10,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:10,641] [INFO] DFAST_QC result json was written to GCF_014335175.1_LK23_genomic.fna/dqc_result.json
[2024-01-24 13:47:10,642] [INFO] DFAST_QC completed!
[2024-01-24 13:47:10,642] [INFO] Total running time: 0h0m52s