[2024-01-24 14:19:01,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference
[2024-01-24 14:19:02,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,508] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,508] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd1d8ff8-020b-41d2-b05a-d08a0404fda5/GCF_900187315.1_52087_C01_genomic.fna.gz | prodigal -d GCF_900187315.1_52087_C01_genomic.fna/cds.fna -a GCF_900187315.1_52087_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:08,709] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:08,710] [INFO] Task started: HMMsearch
[2024-01-24 14:19:08,710] [INFO] Running command: hmmsearch --tblout GCF_900187315.1_52087_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/reference_markers.hmm GCF_900187315.1_52087_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:09,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:09,012] [INFO] Found 6/6 markers.
[2024-01-24 14:19:09,041] [INFO] Query marker FASTA was written to GCF_900187315.1_52087_C01_genomic.fna/markers.fasta
[2024-01-24 14:19:09,042] [INFO] Task started: Blastn
[2024-01-24 14:19:09,042] [INFO] Running command: blastn -query GCF_900187315.1_52087_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/reference_markers.fasta -out GCF_900187315.1_52087_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:09,675] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:09,679] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:09,680] [INFO] Target genome list was writen to GCF_900187315.1_52087_C01_genomic.fna/target_genomes.txt
[2024-01-24 14:19:09,690] [INFO] Task started: fastANI
[2024-01-24 14:19:09,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1d8ff8-020b-41d2-b05a-d08a0404fda5/GCF_900187315.1_52087_C01_genomic.fna.gz --refList GCF_900187315.1_52087_C01_genomic.fna/target_genomes.txt --output GCF_900187315.1_52087_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:19,091] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:19,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:19,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:19,103] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:19,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:19,104] [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 welshimeri	strain=NCTC11857	GCA_900187315.1	1643	1643	type	True	100.0	938	938	95	conclusive
Listeria welshimeri	strain=SLCC5334	GCA_000060285.1	1643	1643	type	True	99.9988	938	938	95	conclusive
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	87.7944	788	938	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	87.6592	799	938	95	below_threshold
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	87.5865	766	938	95	below_threshold
Listeria innocua	strain=2010L-2059	GCA_017363615.2	1642	1642	claderef	True	87.4563	799	938	95	below_threshold
Listeria monocytogenes	strain=NCTC10357	GCA_900187225.1	1639	1639	type	True	87.2952	778	938	95	below_threshold
Listeria monocytogenes	strain=FSL F6-684	GCA_000743465.1	1639	1639	type	True	87.2058	772	938	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	87.1714	773	938	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	87.1533	774	938	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	87.1238	744	938	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	86.9852	743	938	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	86.8571	757	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:19,106] [INFO] DFAST Taxonomy check result was written to GCF_900187315.1_52087_C01_genomic.fna/tc_result.tsv
[2024-01-24 14:19:19,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:19,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:19,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/checkm_data
[2024-01-24 14:19:19,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:19,138] [INFO] Task started: CheckM
[2024-01-24 14:19:19,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187315.1_52087_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187315.1_52087_C01_genomic.fna/checkm_input GCF_900187315.1_52087_C01_genomic.fna/checkm_result
[2024-01-24 14:19:44,601] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:44,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:44,620] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:44,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:44,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187315.1_52087_C01_genomic.fna/markers.fasta)
[2024-01-24 14:19:44,622] [INFO] Task started: Blastn
[2024-01-24 14:19:44,622] [INFO] Running command: blastn -query GCF_900187315.1_52087_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg98b308cf-5219-4971-a9eb-e1cd15c09762/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187315.1_52087_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:45,433] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:45,442] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:45,443] [INFO] Target genome list was writen to GCF_900187315.1_52087_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:45,464] [INFO] Task started: fastANI
[2024-01-24 14:19:45,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1d8ff8-020b-41d2-b05a-d08a0404fda5/GCF_900187315.1_52087_C01_genomic.fna.gz --refList GCF_900187315.1_52087_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187315.1_52087_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:54,428] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:54,439] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:54,439] [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_000060285.1	s__Listeria welshimeri	99.9988	938	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.96	98.73	0.93	0.90	49	conclusive
GCF_015276835.1	s__Listeria innocua	87.5102	790	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	-
GCF_900187225.1	s__Listeria monocytogenes	87.2952	778	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_000307025.1	s__Listeria monocytogenes_B	87.1886	802	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.46	95.21	0.96	0.90	1699	-
GCF_014229245.1	s__Listeria farberi	87.1694	766	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	99.31	0.93	0.92	5	-
GCF_014229645.1	s__Listeria sp014229645	87.1238	744	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282665.1	s__Listeria monocytogenes_C	87.093	763	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	95.79	95.20	0.93	0.91	176	-
GCF_014229095.1	s__Listeria cayugensis	86.8529	747	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
GCF_014224155.1	s__Listeria cossartiae	86.7981	754	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
GCF_000027145.1	s__Listeria seeligeri	84.229	704	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.08	96.23	0.92	0.88	167	-
GCF_900187025.1	s__Listeria ivanovii	84.22	689	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.75	99.44	0.99	0.97	26	-
GCF_014322765.1	s__Listeria immobilis	83.5791	659	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	97.95	0.95	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:54,446] [INFO] GTDB search result was written to GCF_900187315.1_52087_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:54,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:54,451] [INFO] DFAST_QC result json was written to GCF_900187315.1_52087_C01_genomic.fna/dqc_result.json
[2024-01-24 14:19:54,451] [INFO] DFAST_QC completed!
[2024-01-24 14:19:54,451] [INFO] Total running time: 0h0m53s