[2024-01-25 18:08:35,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference
[2024-01-25 18:08:36,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,764] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,764] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa759f50-ef79-431e-b38c-4e2192da3092/GCF_000525955.1_Lweihenstaphanensis_genomic.fna.gz | prodigal -d GCF_000525955.1_Lweihenstaphanensis_genomic.fna/cds.fna -a GCF_000525955.1_Lweihenstaphanensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:43,476] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:43,476] [INFO] Task started: HMMsearch
[2024-01-25 18:08:43,476] [INFO] Running command: hmmsearch --tblout GCF_000525955.1_Lweihenstaphanensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/reference_markers.hmm GCF_000525955.1_Lweihenstaphanensis_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:43,717] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:43,718] [INFO] Found 6/6 markers.
[2024-01-25 18:08:43,750] [INFO] Query marker FASTA was written to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/markers.fasta
[2024-01-25 18:08:43,750] [INFO] Task started: Blastn
[2024-01-25 18:08:43,750] [INFO] Running command: blastn -query GCF_000525955.1_Lweihenstaphanensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/reference_markers.fasta -out GCF_000525955.1_Lweihenstaphanensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:44,308] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:44,311] [INFO] Selected 12 target genomes.
[2024-01-25 18:08:44,312] [INFO] Target genome list was writen to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/target_genomes.txt
[2024-01-25 18:08:44,321] [INFO] Task started: fastANI
[2024-01-25 18:08:44,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa759f50-ef79-431e-b38c-4e2192da3092/GCF_000525955.1_Lweihenstaphanensis_genomic.fna.gz --refList GCF_000525955.1_Lweihenstaphanensis_genomic.fna/target_genomes.txt --output GCF_000525955.1_Lweihenstaphanensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:53,345] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:53,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:53,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:53,352] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:53,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:53,352] [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
Listeria weihenstephanensis	strain=FSL R9-0317	GCA_000525955.1	1006155	1006155	type	True	100.0	1092	1093	95	conclusive
Listeria portnoyi	strain=FSL L7-1582	GCA_014322795.1	2713504	2713504	type	True	86.4492	747	1093	95	below_threshold
Listeria rustica	strain=FSL W9-0585	GCA_013820765.1	2713503	2713503	type	True	86.3311	782	1093	95	below_threshold
Listeria newyorkensis	strain=NCTC13937	GCA_900461625.1	1497681	1497681	type	True	85.0047	782	1093	95	below_threshold
Listeria newyorkensis	strain=FSL M6-0635	GCA_000766145.1	1497681	1497681	type	True	84.972	774	1093	95	below_threshold
Listeria cornellensis	strain=FSL F6-0969	GCA_000525855.1	1494961	1494961	type	True	84.6465	753	1093	95	below_threshold
Listeria grandensis	strain=FSL F6-0971	GCA_000525835.1	1494963	1494963	type	True	83.3569	668	1093	95	below_threshold
Listeria ivanovii subsp. ivanovii	strain=PAM 55	GCA_000252975.1	202751	1638	claderef	True	77.6752	167	1093	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	77.6133	166	1093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:53,355] [INFO] DFAST Taxonomy check result was written to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/tc_result.tsv
[2024-01-25 18:08:53,355] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:53,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:53,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/checkm_data
[2024-01-25 18:08:53,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:53,391] [INFO] Task started: CheckM
[2024-01-25 18:08:53,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000525955.1_Lweihenstaphanensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000525955.1_Lweihenstaphanensis_genomic.fna/checkm_input GCF_000525955.1_Lweihenstaphanensis_genomic.fna/checkm_result
[2024-01-25 18:09:17,813] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:17,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:17,831] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:17,832] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:17,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000525955.1_Lweihenstaphanensis_genomic.fna/markers.fasta)
[2024-01-25 18:09:17,832] [INFO] Task started: Blastn
[2024-01-25 18:09:17,832] [INFO] Running command: blastn -query GCF_000525955.1_Lweihenstaphanensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cee72e7-95c5-41a9-bf2f-4cfa439e226b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000525955.1_Lweihenstaphanensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:18,594] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:18,596] [INFO] Selected 6 target genomes.
[2024-01-25 18:09:18,597] [INFO] Target genome list was writen to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:18,605] [INFO] Task started: fastANI
[2024-01-25 18:09:18,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa759f50-ef79-431e-b38c-4e2192da3092/GCF_000525955.1_Lweihenstaphanensis_genomic.fna.gz --refList GCF_000525955.1_Lweihenstaphanensis_genomic.fna/target_genomes_gtdb.txt --output GCF_000525955.1_Lweihenstaphanensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:24,169] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:24,175] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:24,175] [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_003534205.1	s__Listeria_A weihenstephanensis	99.9758	1092	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.01	98.05	0.93	0.87	3	conclusive
GCF_014322795.1	s__Listeria_A portnoyi	86.4732	746	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013820765.1	s__Listeria_A rustica	86.3132	785	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766145.1	s__Listeria_A newyorkensis	84.9855	773	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	98.92	95.80	0.93	0.85	8	-
GCF_000525855.1	s__Listeria_A cornellensis	84.6366	754	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000525835.1	s__Listeria_A grandensis	83.3545	668	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	97.47	97.36	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:24,176] [INFO] GTDB search result was written to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:24,177] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:24,179] [INFO] DFAST_QC result json was written to GCF_000525955.1_Lweihenstaphanensis_genomic.fna/dqc_result.json
[2024-01-25 18:09:24,179] [INFO] DFAST_QC completed!
[2024-01-25 18:09:24,179] [INFO] Total running time: 0h0m49s