[2024-01-25 19:46:35,676] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:35,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:35,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference
[2024-01-25 19:46:36,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:36,812] [INFO] Task started: Prodigal
[2024-01-25 19:46:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg061c4baa-a0a6-4b81-8c85-0aac6ab93652/GCF_000428865.1_ASM42886v1_genomic.fna.gz | prodigal -d GCF_000428865.1_ASM42886v1_genomic.fna/cds.fna -a GCF_000428865.1_ASM42886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:39,786] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:39,786] [INFO] Task started: HMMsearch
[2024-01-25 19:46:39,786] [INFO] Running command: hmmsearch --tblout GCF_000428865.1_ASM42886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/reference_markers.hmm GCF_000428865.1_ASM42886v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:40,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:40,030] [INFO] Found 6/6 markers.
[2024-01-25 19:46:40,048] [INFO] Query marker FASTA was written to GCF_000428865.1_ASM42886v1_genomic.fna/markers.fasta
[2024-01-25 19:46:40,048] [INFO] Task started: Blastn
[2024-01-25 19:46:40,048] [INFO] Running command: blastn -query GCF_000428865.1_ASM42886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/reference_markers.fasta -out GCF_000428865.1_ASM42886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:40,591] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:40,594] [INFO] Selected 23 target genomes.
[2024-01-25 19:46:40,594] [INFO] Target genome list was writen to GCF_000428865.1_ASM42886v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:40,609] [INFO] Task started: fastANI
[2024-01-25 19:46:40,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg061c4baa-a0a6-4b81-8c85-0aac6ab93652/GCF_000428865.1_ASM42886v1_genomic.fna.gz --refList GCF_000428865.1_ASM42886v1_genomic.fna/target_genomes.txt --output GCF_000428865.1_ASM42886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:48,979] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:48,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:48,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:48,983] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:48,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:48,983] [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
Eremococcus coleocola	strain=DSM 15696	GCA_000428865.1	88132	88132	type	True	100.0	595	597	95	conclusive
Globicatella sulfidifaciens	strain=DSM 15739	GCA_900167405.1	136093	136093	type	True	77.3091	61	597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:48,984] [INFO] DFAST Taxonomy check result was written to GCF_000428865.1_ASM42886v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:48,985] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:48,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:48,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/checkm_data
[2024-01-25 19:46:48,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:49,007] [INFO] Task started: CheckM
[2024-01-25 19:46:49,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428865.1_ASM42886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428865.1_ASM42886v1_genomic.fna/checkm_input GCF_000428865.1_ASM42886v1_genomic.fna/checkm_result
[2024-01-25 19:47:04,533] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:04,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:04,548] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:04,548] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:04,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428865.1_ASM42886v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:04,548] [INFO] Task started: Blastn
[2024-01-25 19:47:04,548] [INFO] Running command: blastn -query GCF_000428865.1_ASM42886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10890c41-b64a-4a91-8471-3f21cf9b2a5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428865.1_ASM42886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:05,305] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:05,308] [INFO] Selected 28 target genomes.
[2024-01-25 19:47:05,309] [INFO] Target genome list was writen to GCF_000428865.1_ASM42886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:05,343] [INFO] Task started: fastANI
[2024-01-25 19:47:05,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg061c4baa-a0a6-4b81-8c85-0aac6ab93652/GCF_000428865.1_ASM42886v1_genomic.fna.gz --refList GCF_000428865.1_ASM42886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428865.1_ASM42886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:17,869] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:17,873] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:17,873] [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_000428865.1	s__Eremococcus coleocola	100.0	595	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Eremococcus	95.0	98.93	98.93	0.90	0.90	2	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:47:17,875] [INFO] GTDB search result was written to GCF_000428865.1_ASM42886v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:17,876] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:17,877] [INFO] DFAST_QC result json was written to GCF_000428865.1_ASM42886v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:17,877] [INFO] DFAST_QC completed!
[2024-01-25 19:47:17,878] [INFO] Total running time: 0h0m42s