[2024-01-24 13:01:12,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference
[2024-01-24 13:01:13,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,546] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg2db60ed0-6713-44fd-8428-dc1018605274/GCF_000060285.1_ASM6028v1_genomic.fna.gz | prodigal -d GCF_000060285.1_ASM6028v1_genomic.fna/cds.fna -a GCF_000060285.1_ASM6028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:19,519] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:19,519] [INFO] Task started: HMMsearch
[2024-01-24 13:01:19,519] [INFO] Running command: hmmsearch --tblout GCF_000060285.1_ASM6028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/reference_markers.hmm GCF_000060285.1_ASM6028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:19,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:19,831] [INFO] Found 6/6 markers.
[2024-01-24 13:01:19,883] [INFO] Query marker FASTA was written to GCF_000060285.1_ASM6028v1_genomic.fna/markers.fasta
[2024-01-24 13:01:19,883] [INFO] Task started: Blastn
[2024-01-24 13:01:19,883] [INFO] Running command: blastn -query GCF_000060285.1_ASM6028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/reference_markers.fasta -out GCF_000060285.1_ASM6028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:20,529] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:20,532] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:20,533] [INFO] Target genome list was writen to GCF_000060285.1_ASM6028v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:20,538] [INFO] Task started: fastANI
[2024-01-24 13:01:20,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg2db60ed0-6713-44fd-8428-dc1018605274/GCF_000060285.1_ASM6028v1_genomic.fna.gz --refList GCF_000060285.1_ASM6028v1_genomic.fna/target_genomes.txt --output GCF_000060285.1_ASM6028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:29,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:29,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:29,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:29,310] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:29,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:29,311] [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=SLCC5334	GCA_000060285.1	1643	1643	type	True	100.0	937	938	95	conclusive
Listeria welshimeri	strain=NCTC11857	GCA_900187315.1	1643	1643	type	True	99.9991	937	938	95	conclusive
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	87.7654	787	938	95	below_threshold
Listeria innocua	strain=2010L-2059	GCA_017363615.2	1642	1642	claderef	True	87.6238	796	938	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	87.6079	783	938	95	below_threshold
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	87.5432	782	938	95	below_threshold
Listeria monocytogenes	strain=NCTC10357	GCA_900187225.1	1639	1639	type	True	87.3208	777	938	95	below_threshold
Listeria monocytogenes	strain=FSL F6-684	GCA_000743465.1	1639	1639	type	True	87.2676	776	938	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	87.1192	779	938	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	87.0989	778	938	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	87.0543	748	938	95	below_threshold
Listeria monocytogenes	strain=2014L-6393	GCA_013626145.1	1639	1639	claderef	True	86.934	753	938	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	86.8385	775	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:29,313] [INFO] DFAST Taxonomy check result was written to GCF_000060285.1_ASM6028v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:29,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:29,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:29,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/checkm_data
[2024-01-24 13:01:29,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:29,345] [INFO] Task started: CheckM
[2024-01-24 13:01:29,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000060285.1_ASM6028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000060285.1_ASM6028v1_genomic.fna/checkm_input GCF_000060285.1_ASM6028v1_genomic.fna/checkm_result
[2024-01-24 13:01:53,262] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:53,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:53,280] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:53,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:53,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000060285.1_ASM6028v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:53,281] [INFO] Task started: Blastn
[2024-01-24 13:01:53,281] [INFO] Running command: blastn -query GCF_000060285.1_ASM6028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a28003d-304c-4e90-86ab-8fab26070ebf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000060285.1_ASM6028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:54,089] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:54,092] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:54,092] [INFO] Target genome list was writen to GCF_000060285.1_ASM6028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:54,102] [INFO] Task started: fastANI
[2024-01-24 13:01:54,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg2db60ed0-6713-44fd-8428-dc1018605274/GCF_000060285.1_ASM6028v1_genomic.fna.gz --refList GCF_000060285.1_ASM6028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000060285.1_ASM6028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:02,626] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:02,637] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:02,637] [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	100.0	937	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	87.4944	780	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	87.3207	777	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	87.2595	796	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	87.1069	768	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	87.0543	748	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	86.9995	773	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	86.8655	743	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	86.758	751	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_900187025.1	s__Listeria ivanovii	84.1358	692	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_000027145.1	s__Listeria seeligeri	84.0829	716	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_014322765.1	s__Listeria immobilis	83.6641	653	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 13:02:02,639] [INFO] GTDB search result was written to GCF_000060285.1_ASM6028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:02,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:02,642] [INFO] DFAST_QC result json was written to GCF_000060285.1_ASM6028v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:02,643] [INFO] DFAST_QC completed!
[2024-01-24 13:02:02,643] [INFO] Total running time: 0h0m50s