[2024-01-24 12:40:03,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:03,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:03,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference
[2024-01-24 12:40:05,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:05,031] [INFO] Task started: Prodigal
[2024-01-24 12:40:05,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb125a34-1c17-46cb-9e39-7091824f573e/GCF_003052295.1_ASM305229v1_genomic.fna.gz | prodigal -d GCF_003052295.1_ASM305229v1_genomic.fna/cds.fna -a GCF_003052295.1_ASM305229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:10,821] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:10,821] [INFO] Task started: HMMsearch
[2024-01-24 12:40:10,821] [INFO] Running command: hmmsearch --tblout GCF_003052295.1_ASM305229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/reference_markers.hmm GCF_003052295.1_ASM305229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:11,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:11,047] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfb125a34-1c17-46cb-9e39-7091824f573e/GCF_003052295.1_ASM305229v1_genomic.fna.gz]
[2024-01-24 12:40:11,069] [INFO] Query marker FASTA was written to GCF_003052295.1_ASM305229v1_genomic.fna/markers.fasta
[2024-01-24 12:40:11,070] [INFO] Task started: Blastn
[2024-01-24 12:40:11,070] [INFO] Running command: blastn -query GCF_003052295.1_ASM305229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/reference_markers.fasta -out GCF_003052295.1_ASM305229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:11,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:11,655] [INFO] Selected 5 target genomes.
[2024-01-24 12:40:11,656] [INFO] Target genome list was writen to GCF_003052295.1_ASM305229v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:11,659] [INFO] Task started: fastANI
[2024-01-24 12:40:11,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb125a34-1c17-46cb-9e39-7091824f573e/GCF_003052295.1_ASM305229v1_genomic.fna.gz --refList GCF_003052295.1_ASM305229v1_genomic.fna/target_genomes.txt --output GCF_003052295.1_ASM305229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:14,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:14,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:14,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:14,884] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:14,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:14,884] [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
Trichococcus paludicola	strain=B7-2	GCA_003052295.1	2052942	2052942	type	True	100.0	643	643	95	conclusive
Trichococcus collinsii	strain=DSM 14526	GCA_900107505.1	157076	157076	type	True	92.717	575	643	95	below_threshold
Trichococcus alkaliphilus	strain=B5	GCA_003008695.1	2052943	2052943	type	True	92.6451	554	643	95	below_threshold
Trichococcus shcherbakoviae subsp. psychrophilus	strain=SKBG	GCA_006370295.1	2585775	2094020	type	True	91.9552	564	643	95	below_threshold
Trichococcus patagoniensis	strain=DSM 18806	GCA_003051085.1	382641	382641	type	True	90.5171	541	643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:14,886] [INFO] DFAST Taxonomy check result was written to GCF_003052295.1_ASM305229v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:14,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:14,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:14,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/checkm_data
[2024-01-24 12:40:14,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:14,910] [INFO] Task started: CheckM
[2024-01-24 12:40:14,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003052295.1_ASM305229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003052295.1_ASM305229v1_genomic.fna/checkm_input GCF_003052295.1_ASM305229v1_genomic.fna/checkm_result
[2024-01-24 12:40:38,444] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:38,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:38,467] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:38,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:38,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003052295.1_ASM305229v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:38,469] [INFO] Task started: Blastn
[2024-01-24 12:40:38,469] [INFO] Running command: blastn -query GCF_003052295.1_ASM305229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg268a31eb-618c-436e-809f-1cb0d9d677ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003052295.1_ASM305229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:39,218] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:39,222] [INFO] Selected 5 target genomes.
[2024-01-24 12:40:39,222] [INFO] Target genome list was writen to GCF_003052295.1_ASM305229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:39,227] [INFO] Task started: fastANI
[2024-01-24 12:40:39,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb125a34-1c17-46cb-9e39-7091824f573e/GCF_003052295.1_ASM305229v1_genomic.fna.gz --refList GCF_003052295.1_ASM305229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003052295.1_ASM305229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:42,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:42,526] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:42,527] [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_003052295.1	s__Trichococcus paludicola	100.0	643	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107505.1	s__Trichococcus collinsii	92.6862	576	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003008695.1	s__Trichococcus alkaliphilus	92.6451	554	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002155105.1	s__Trichococcus shcherbakoviae	91.7891	566	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	97.18	96.59	0.87	0.86	3	-
GCF_003051085.1	s__Trichococcus patagoniensis	90.5293	540	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Trichococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:42,529] [INFO] GTDB search result was written to GCF_003052295.1_ASM305229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:42,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:42,534] [INFO] DFAST_QC result json was written to GCF_003052295.1_ASM305229v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:42,534] [INFO] DFAST_QC completed!
[2024-01-24 12:40:42,534] [INFO] Total running time: 0h0m39s