[2024-01-24 13:32:34,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference
[2024-01-24 13:32:36,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,258] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg84b0bce1-3da4-4995-acdd-2107db0b58bb/GCF_000425085.1_ASM42508v1_genomic.fna.gz | prodigal -d GCF_000425085.1_ASM42508v1_genomic.fna/cds.fna -a GCF_000425085.1_ASM42508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:40,569] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:40,569] [INFO] Task started: HMMsearch
[2024-01-24 13:32:40,569] [INFO] Running command: hmmsearch --tblout GCF_000425085.1_ASM42508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/reference_markers.hmm GCF_000425085.1_ASM42508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:40,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:40,868] [INFO] Found 6/6 markers.
[2024-01-24 13:32:40,888] [INFO] Query marker FASTA was written to GCF_000425085.1_ASM42508v1_genomic.fna/markers.fasta
[2024-01-24 13:32:40,889] [INFO] Task started: Blastn
[2024-01-24 13:32:40,889] [INFO] Running command: blastn -query GCF_000425085.1_ASM42508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/reference_markers.fasta -out GCF_000425085.1_ASM42508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,611] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,615] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:41,616] [INFO] Target genome list was writen to GCF_000425085.1_ASM42508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,618] [INFO] Task started: fastANI
[2024-01-24 13:32:41,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b0bce1-3da4-4995-acdd-2107db0b58bb/GCF_000425085.1_ASM42508v1_genomic.fna.gz --refList GCF_000425085.1_ASM42508v1_genomic.fna/target_genomes.txt --output GCF_000425085.1_ASM42508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:45,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:45,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:45,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:45,567] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:45,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:45,568] [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
Aerococcus urinaeequi	strain=DSM 20341	GCA_000425085.1	51665	51665	suspected-type	True	100.0	658	659	95	conclusive
Aerococcus urinaeequi	strain=CCUG28094	GCA_001543205.1	51665	51665	type	True	99.9943	658	659	95	conclusive
Aerococcus viridans	strain=ATCC 11563	GCA_000178435.1	1377	1377	suspected-type	True	93.9596	506	659	95	below_threshold
Aerococcus viridans	strain=NCTC8251	GCA_900445095.1	1377	1377	suspected-type	True	93.7852	551	659	95	below_threshold
Aerococcus viridans	strain=CCUG4311	GCA_001543285.1	1377	1377	suspected-type	True	93.7701	547	659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,569] [INFO] DFAST Taxonomy check result was written to GCF_000425085.1_ASM42508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:45,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:45,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:45,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/checkm_data
[2024-01-24 13:32:45,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:45,593] [INFO] Task started: CheckM
[2024-01-24 13:32:45,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425085.1_ASM42508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425085.1_ASM42508v1_genomic.fna/checkm_input GCF_000425085.1_ASM42508v1_genomic.fna/checkm_result
[2024-01-24 13:33:06,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:06,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:06,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:06,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425085.1_ASM42508v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:06,471] [INFO] Task started: Blastn
[2024-01-24 13:33:06,471] [INFO] Running command: blastn -query GCF_000425085.1_ASM42508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg468bde49-9198-4ea2-8f5c-8f2fef8e97ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425085.1_ASM42508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,250] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:07,250] [INFO] Target genome list was writen to GCF_000425085.1_ASM42508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:07,255] [INFO] Task started: fastANI
[2024-01-24 13:33:07,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b0bce1-3da4-4995-acdd-2107db0b58bb/GCF_000425085.1_ASM42508v1_genomic.fna.gz --refList GCF_000425085.1_ASM42508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425085.1_ASM42508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:10,342] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,348] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:10,348] [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_001543205.1	s__Aerococcus urinaeequi	99.9943	658	659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	96.56	95.91	0.88	0.83	18	conclusive
GCF_002083135.2	s__Aerococcus viridans_C	94.09	551	659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543285.1	s__Aerococcus viridans	93.7701	547	659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	99.21	97.63	0.94	0.82	4	-
GCA_002440555.1	s__Aerococcus sp002440555	92.519	491	659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871935.1	s__Aerococcus viridans_B	85.8189	469	659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	98.96	98.96	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,350] [INFO] GTDB search result was written to GCF_000425085.1_ASM42508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:10,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:10,353] [INFO] DFAST_QC result json was written to GCF_000425085.1_ASM42508v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:10,353] [INFO] DFAST_QC completed!
[2024-01-24 13:33:10,353] [INFO] Total running time: 0h0m35s