[2024-01-25 19:31:51,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference
[2024-01-25 19:31:52,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,658] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg6442b6c5-dc67-40e4-8af3-2366b7fbb06e/GCF_000092365.1_ASM9236v1_genomic.fna.gz | prodigal -d GCF_000092365.1_ASM9236v1_genomic.fna/cds.fna -a GCF_000092365.1_ASM9236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:31:57,992] [INFO] Task succeeded: Prodigal
[2024-01-25 19:31:57,993] [INFO] Task started: HMMsearch
[2024-01-25 19:31:57,993] [INFO] Running command: hmmsearch --tblout GCF_000092365.1_ASM9236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/reference_markers.hmm GCF_000092365.1_ASM9236v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:31:58,175] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:31:58,176] [INFO] Found 6/6 markers.
[2024-01-25 19:31:58,195] [INFO] Query marker FASTA was written to GCF_000092365.1_ASM9236v1_genomic.fna/markers.fasta
[2024-01-25 19:31:58,196] [INFO] Task started: Blastn
[2024-01-25 19:31:58,196] [INFO] Running command: blastn -query GCF_000092365.1_ASM9236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/reference_markers.fasta -out GCF_000092365.1_ASM9236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:58,804] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:58,807] [INFO] Selected 17 target genomes.
[2024-01-25 19:31:58,807] [INFO] Target genome list was writen to GCF_000092365.1_ASM9236v1_genomic.fna/target_genomes.txt
[2024-01-25 19:31:58,814] [INFO] Task started: fastANI
[2024-01-25 19:31:58,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg6442b6c5-dc67-40e4-8af3-2366b7fbb06e/GCF_000092365.1_ASM9236v1_genomic.fna.gz --refList GCF_000092365.1_ASM9236v1_genomic.fna/target_genomes.txt --output GCF_000092365.1_ASM9236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:06,303] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:06,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:06,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:06,310] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:32:06,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:06,310] [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
Arcanobacterium haemolyticum	strain=DSM 20595	GCA_000092365.1	28264	28264	type	True	100.0	661	662	95	conclusive
Arcanobacterium haemolyticum	strain=NCTC8452	GCA_900475915.1	28264	28264	type	True	99.9898	661	662	95	conclusive
Arcanobacterium phocisimile	strain=DSM 26142	GCA_016904675.1	1302235	1302235	type	True	80.1345	195	662	95	below_threshold
Arcanobacterium phocae	strain=DSM 10002	GCA_900105865.1	131112	131112	suspected-type	True	79.5296	185	662	95	below_threshold
Arcanobacterium pinnipediorum	strain=DSM 28752	GCA_023973165.1	1503041	1503041	type	True	79.331	155	662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:06,311] [INFO] DFAST Taxonomy check result was written to GCF_000092365.1_ASM9236v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:06,312] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:06,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:06,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/checkm_data
[2024-01-25 19:32:06,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:06,335] [INFO] Task started: CheckM
[2024-01-25 19:32:06,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092365.1_ASM9236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092365.1_ASM9236v1_genomic.fna/checkm_input GCF_000092365.1_ASM9236v1_genomic.fna/checkm_result
[2024-01-25 19:32:26,599] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:26,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:26,614] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:26,614] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:26,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092365.1_ASM9236v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:26,615] [INFO] Task started: Blastn
[2024-01-25 19:32:26,615] [INFO] Running command: blastn -query GCF_000092365.1_ASM9236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8565f769-bfd3-40d7-b9e1-de1b91cb774f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092365.1_ASM9236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:27,545] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:27,548] [INFO] Selected 21 target genomes.
[2024-01-25 19:32:27,548] [INFO] Target genome list was writen to GCF_000092365.1_ASM9236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:27,560] [INFO] Task started: fastANI
[2024-01-25 19:32:27,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg6442b6c5-dc67-40e4-8af3-2366b7fbb06e/GCF_000092365.1_ASM9236v1_genomic.fna.gz --refList GCF_000092365.1_ASM9236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092365.1_ASM9236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:36,783] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:36,789] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:36,789] [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_000092365.1	s__Arcanobacterium haemolyticum	100.0	662	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.39	98.67	0.98	0.96	4	conclusive
GCF_012563545.1	s__Arcanobacterium sp012563545	80.5161	169	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904675.1	s__Arcanobacterium phocisimile	80.1592	195	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105865.1	s__Arcanobacterium phocae	79.5215	185	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.03	98.90	0.93	0.90	5	-
GCF_018913465.1	s__Arcanobacterium phocae_A	79.1039	169	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	96.34	96.10	0.91	0.89	37	-
GCF_001469025.1	s__Trueperella bernardiae	77.9759	64	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCA_012516575.1	s__Arcanobacterium sp012516575	77.9445	56	662	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:36,792] [INFO] GTDB search result was written to GCF_000092365.1_ASM9236v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:36,792] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:36,795] [INFO] DFAST_QC result json was written to GCF_000092365.1_ASM9236v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:36,795] [INFO] DFAST_QC completed!
[2024-01-25 19:32:36,795] [INFO] Total running time: 0h0m45s