[2024-01-24 12:13:58,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:58,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:58,215] [INFO] DQC Reference Directory: /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference
[2024-01-24 12:13:59,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:59,721] [INFO] Task started: Prodigal
[2024-01-24 12:13:59,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg5341abae-5de5-49f3-8345-58ecf4a84e9e/GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna.gz | prodigal -d GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/cds.fna -a GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:07,630] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:07,630] [INFO] Task started: HMMsearch
[2024-01-24 12:14:07,630] [INFO] Running command: hmmsearch --tblout GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/reference_markers.hmm GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:07,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:07,961] [INFO] Found 6/6 markers.
[2024-01-24 12:14:07,992] [INFO] Query marker FASTA was written to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/markers.fasta
[2024-01-24 12:14:07,992] [INFO] Task started: Blastn
[2024-01-24 12:14:07,992] [INFO] Running command: blastn -query GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/reference_markers.fasta -out GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:08,644] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:08,647] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:08,647] [INFO] Target genome list was writen to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/target_genomes.txt
[2024-01-24 12:14:08,652] [INFO] Task started: fastANI
[2024-01-24 12:14:08,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg5341abae-5de5-49f3-8345-58ecf4a84e9e/GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna.gz --refList GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/target_genomes.txt --output GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:17,421] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:17,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:17,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:17,428] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:17,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:17,429] [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 cornellensis	strain=FSL F6-0969	GCA_000525855.1	1494961	1494961	type	True	100.0	1075	1080	95	conclusive
Listeria newyorkensis	strain=FSL M6-0635	GCA_000766145.1	1497681	1497681	type	True	90.915	876	1080	95	below_threshold
Listeria newyorkensis	strain=NCTC13937	GCA_900461625.1	1497681	1497681	type	True	90.8533	877	1080	95	below_threshold
Listeria rustica	strain=FSL W9-0585	GCA_013820765.1	2713503	2713503	type	True	89.5339	852	1080	95	below_threshold
Listeria portnoyi	strain=FSL L7-1582	GCA_014322795.1	2713504	2713504	type	True	89.2048	801	1080	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	77.6171	182	1080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:17,431] [INFO] DFAST Taxonomy check result was written to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/tc_result.tsv
[2024-01-24 12:14:17,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:17,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:17,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/checkm_data
[2024-01-24 12:14:17,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:17,473] [INFO] Task started: CheckM
[2024-01-24 12:14:17,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/checkm_input GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/checkm_result
[2024-01-24 12:14:47,982] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:47,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:48,015] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:48,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:48,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/markers.fasta)
[2024-01-24 12:14:48,016] [INFO] Task started: Blastn
[2024-01-24 12:14:48,016] [INFO] Running command: blastn -query GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54c3a7a-f879-4419-8d73-14c70e5475ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,775] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,778] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:48,778] [INFO] Target genome list was writen to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:48,787] [INFO] Task started: fastANI
[2024-01-24 12:14:48,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg5341abae-5de5-49f3-8345-58ecf4a84e9e/GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna.gz --refList GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/target_genomes_gtdb.txt --output GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:56,169] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:56,176] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:56,176] [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_000525855.1	s__Listeria_A cornellensis	100.0	1075	1080	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000766145.1	s__Listeria_A newyorkensis	90.915	876	1080	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_013820765.1	s__Listeria_A rustica	89.5162	853	1080	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_014322795.1	s__Listeria_A portnoyi	89.201	802	1080	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	85.1349	755	1080	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	97.47	97.36	0.88	0.88	4	-
GCF_003534205.1	s__Listeria_A weihenstephanensis	84.7116	777	1080	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.01	98.05	0.93	0.87	3	-
GCF_000525975.1	s__Listeria_A rocourtiae	84.0098	728	1080	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A	95.0	99.32	98.60	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:56,181] [INFO] GTDB search result was written to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:56,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:56,184] [INFO] DFAST_QC result json was written to GCF_000525855.1_Listeriaceae_bacterium_FSL_F6-969_genomic.fna/dqc_result.json
[2024-01-24 12:14:56,185] [INFO] DFAST_QC completed!
[2024-01-24 12:14:56,185] [INFO] Total running time: 0h0m58s