[2024-01-24 11:59:22,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference
[2024-01-24 11:59:25,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,640] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgef0eaa08-64c8-4108-b851-57e0411b82ed/GCF_900183385.1_CLIP_2016_00682_genomic.fna.gz | prodigal -d GCF_900183385.1_CLIP_2016_00682_genomic.fna/cds.fna -a GCF_900183385.1_CLIP_2016_00682_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:33,618] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:33,619] [INFO] Task started: HMMsearch
[2024-01-24 11:59:33,619] [INFO] Running command: hmmsearch --tblout GCF_900183385.1_CLIP_2016_00682_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/reference_markers.hmm GCF_900183385.1_CLIP_2016_00682_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:33,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:33,893] [INFO] Found 6/6 markers.
[2024-01-24 11:59:33,941] [INFO] Query marker FASTA was written to GCF_900183385.1_CLIP_2016_00682_genomic.fna/markers.fasta
[2024-01-24 11:59:33,942] [INFO] Task started: Blastn
[2024-01-24 11:59:33,942] [INFO] Running command: blastn -query GCF_900183385.1_CLIP_2016_00682_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/reference_markers.fasta -out GCF_900183385.1_CLIP_2016_00682_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:34,550] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:34,554] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:34,555] [INFO] Target genome list was writen to GCF_900183385.1_CLIP_2016_00682_genomic.fna/target_genomes.txt
[2024-01-24 11:59:34,573] [INFO] Task started: fastANI
[2024-01-24 11:59:34,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0eaa08-64c8-4108-b851-57e0411b82ed/GCF_900183385.1_CLIP_2016_00682_genomic.fna.gz --refList GCF_900183385.1_CLIP_2016_00682_genomic.fna/target_genomes.txt --output GCF_900183385.1_CLIP_2016_00682_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:42,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:42,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:42,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:42,583] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:42,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:42,583] [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 costaricensis		GCA_900183385.1	2026604	2026604	type	True	100.0	1036	1040	95	conclusive
Listeria ilorinensis		GCA_913566895.1	2867439	2867439	type	True	85.1255	781	1040	95	below_threshold
Listeria floridensis	strain=FSL S10-1187	GCA_000525875.1	1494962	1494962	type	True	78.4483	155	1040	95	below_threshold
Listeria innocua	strain=2010L-2059	GCA_017363615.2	1642	1642	claderef	True	78.1987	159	1040	95	below_threshold
Listeria fleischmannii subsp. fleischmannii	strain=LU2006-1	GCA_000344175.1	1671902	1069827	type	True	78.0664	157	1040	95	below_threshold
Listeria fleischmannii subsp. coloradonensis	strain=NCTC13938	GCA_900452975.1	1081736	1069827	type	True	78.0229	166	1040	95	below_threshold
Listeria aquatica	strain=FSL S10-1188	GCA_000525795.1	1494960	1494960	type	True	77.9598	151	1040	95	below_threshold
Listeria valentina	strain=CLIP 2019/00642	GCA_011800755.1	2705293	2705293	type	True	77.921	142	1040	95	below_threshold
Listeria monocytogenes	strain=2014L-6256	GCA_013625895.1	1639	1639	claderef	True	77.8811	159	1040	95	below_threshold
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	77.8519	160	1040	95	below_threshold
Listeria fleischmannii subsp. coloradonensis	strain=TTU M1-001	GCA_000252625.2	1081736	1069827	type	True	77.8488	135	1040	95	below_threshold
Listeria swaminathanii	strain=FSL L7-0020	GCA_014229645.1	2713501	2713501	type	True	77.8448	166	1040	95	below_threshold
Listeria innocua	strain=H0996	GCA_017363655.2	1642	1642	claderef	True	77.834	165	1040	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	77.8338	167	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:42,585] [INFO] DFAST Taxonomy check result was written to GCF_900183385.1_CLIP_2016_00682_genomic.fna/tc_result.tsv
[2024-01-24 11:59:42,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:42,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:42,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/checkm_data
[2024-01-24 11:59:42,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:42,625] [INFO] Task started: CheckM
[2024-01-24 11:59:42,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900183385.1_CLIP_2016_00682_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900183385.1_CLIP_2016_00682_genomic.fna/checkm_input GCF_900183385.1_CLIP_2016_00682_genomic.fna/checkm_result
[2024-01-24 12:00:11,784] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:11,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:11,804] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:11,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:11,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900183385.1_CLIP_2016_00682_genomic.fna/markers.fasta)
[2024-01-24 12:00:11,806] [INFO] Task started: Blastn
[2024-01-24 12:00:11,806] [INFO] Running command: blastn -query GCF_900183385.1_CLIP_2016_00682_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f44704f-b903-4b87-b07b-d33e26ee4f9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900183385.1_CLIP_2016_00682_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:12,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:12,590] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:12,590] [INFO] Target genome list was writen to GCF_900183385.1_CLIP_2016_00682_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:12,609] [INFO] Task started: fastANI
[2024-01-24 12:00:12,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0eaa08-64c8-4108-b851-57e0411b82ed/GCF_900183385.1_CLIP_2016_00682_genomic.fna.gz --refList GCF_900183385.1_CLIP_2016_00682_genomic.fna/target_genomes_gtdb.txt --output GCF_900183385.1_CLIP_2016_00682_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:24,439] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:24,458] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:24,459] [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_900183385.1	s__Listeria costaricensis	100.0	1036	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000525875.1	s__Listeria floridensis	78.4733	154	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186125.1	s__Listeria goaensis	78.1824	172	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.59	99.37	0.97	0.94	8	-
GCF_000344175.1	s__Listeria fleischmannii	78.0664	157	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	96.87	95.72	0.93	0.89	9	-
GCF_014229245.1	s__Listeria farberi	78.0572	160	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	99.31	0.93	0.92	5	-
GCF_003369925.1	s__Listeria kieliensis_A	78.0105	153	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	99.04	0.93	0.93	2	-
GCF_900187225.1	s__Listeria monocytogenes	77.9946	169	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_000525795.1	s__Listeria aquatica	77.9598	151	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.71	97.71	0.93	0.93	2	-
GCF_014229095.1	s__Listeria cayugensis	77.9437	171	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
GCF_011800755.1	s__Listeria valentina	77.921	142	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187025.1	s__Listeria ivanovii	77.8618	170	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.75	99.44	0.99	0.97	26	-
GCF_014229645.1	s__Listeria sp014229645	77.8448	166	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806445.1	s__Listeria sp902806445	77.8181	131	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014224155.1	s__Listeria cossartiae	77.7233	182	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.01	97.44	0.96	0.94	9	-
GCF_000060285.1	s__Listeria welshimeri	77.6743	163	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.96	98.73	0.93	0.90	49	-
GCF_000763495.1	s__Listeria londoniensis	77.6669	168	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.36	98.73	0.96	0.94	17	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:24,469] [INFO] GTDB search result was written to GCF_900183385.1_CLIP_2016_00682_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:24,470] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:24,477] [INFO] DFAST_QC result json was written to GCF_900183385.1_CLIP_2016_00682_genomic.fna/dqc_result.json
[2024-01-24 12:00:24,477] [INFO] DFAST_QC completed!
[2024-01-24 12:00:24,477] [INFO] Total running time: 0h1m2s