[2024-01-24 13:57:44,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference
[2024-01-24 13:57:45,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,573] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg691392b6-7b87-41f0-b1d2-12eaeef3f368/GCF_002355155.1_ASM235515v1_genomic.fna.gz | prodigal -d GCF_002355155.1_ASM235515v1_genomic.fna/cds.fna -a GCF_002355155.1_ASM235515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,613] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,613] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,613] [INFO] Running command: hmmsearch --tblout GCF_002355155.1_ASM235515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/reference_markers.hmm GCF_002355155.1_ASM235515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,904] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,935] [INFO] Query marker FASTA was written to GCF_002355155.1_ASM235515v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,935] [INFO] Task started: Blastn
[2024-01-24 13:57:56,935] [INFO] Running command: blastn -query GCF_002355155.1_ASM235515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/reference_markers.fasta -out GCF_002355155.1_ASM235515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,757] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,760] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:57,760] [INFO] Target genome list was writen to GCF_002355155.1_ASM235515v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,763] [INFO] Task started: fastANI
[2024-01-24 13:57:57,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg691392b6-7b87-41f0-b1d2-12eaeef3f368/GCF_002355155.1_ASM235515v1_genomic.fna.gz --refList GCF_002355155.1_ASM235515v1_genomic.fna/target_genomes.txt --output GCF_002355155.1_ASM235515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:02,913] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:02,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:02,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:02,920] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:02,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:02,921] [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 suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	100.0	1179	1179	95	conclusive
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	85.9701	905	1179	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	85.9647	906	1179	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	85.9449	909	1179	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	85.6971	886	1179	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	82.666	723	1179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,922] [INFO] DFAST Taxonomy check result was written to GCF_002355155.1_ASM235515v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:02,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:02,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:02,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/checkm_data
[2024-01-24 13:58:02,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:02,976] [INFO] Task started: CheckM
[2024-01-24 13:58:02,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355155.1_ASM235515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355155.1_ASM235515v1_genomic.fna/checkm_input GCF_002355155.1_ASM235515v1_genomic.fna/checkm_result
[2024-01-24 13:58:41,940] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:41,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:41,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:41,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355155.1_ASM235515v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:41,960] [INFO] Task started: Blastn
[2024-01-24 13:58:41,960] [INFO] Running command: blastn -query GCF_002355155.1_ASM235515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc8de4e-5156-42c3-a052-d7bbc99a63de/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355155.1_ASM235515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,236] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:43,236] [INFO] Target genome list was writen to GCF_002355155.1_ASM235515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:43,275] [INFO] Task started: fastANI
[2024-01-24 13:58:43,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg691392b6-7b87-41f0-b1d2-12eaeef3f368/GCF_002355155.1_ASM235515v1_genomic.fna.gz --refList GCF_002355155.1_ASM235515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355155.1_ASM235515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:49,873] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,885] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:49,885] [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_002355155.1	s__Corynebacterium suranareeae	100.0	1179	1179	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_000011325.1	s__Corynebacterium glutamicum	85.9774	907	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_001643015.1	s__Corynebacterium crudilactis	82.6813	723	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277995.1	s__Corynebacterium deserti	82.3284	628	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344785.1	s__Corynebacterium callunae	80.7077	426	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900169525.1	s__Corynebacterium pacaense	78.8329	193	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.3969	126	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154655.1	s__Corynebacterium kefirresidentii	78.1168	84	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.23	95.39	0.90	0.89	9	-
GCF_003688935.1	s__Corynebacterium macginleyi	77.225	60	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.68	97.89	0.95	0.93	26	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,887] [INFO] GTDB search result was written to GCF_002355155.1_ASM235515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:49,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:49,891] [INFO] DFAST_QC result json was written to GCF_002355155.1_ASM235515v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:49,892] [INFO] DFAST_QC completed!
[2024-01-24 13:58:49,892] [INFO] Total running time: 0h1m6s