[2024-01-24 13:19:26,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,714] [INFO] DQC Reference Directory: /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference
[2024-01-24 13:19:27,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,952] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgabd3eba6-f4a1-454c-86e2-b84325150058/GCF_000344175.1_ASM34417v1_genomic.fna.gz | prodigal -d GCF_000344175.1_ASM34417v1_genomic.fna/cds.fna -a GCF_000344175.1_ASM34417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:33,465] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:33,466] [INFO] Task started: HMMsearch
[2024-01-24 13:19:33,466] [INFO] Running command: hmmsearch --tblout GCF_000344175.1_ASM34417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/reference_markers.hmm GCF_000344175.1_ASM34417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:33,711] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:33,713] [INFO] Found 6/6 markers.
[2024-01-24 13:19:33,742] [INFO] Query marker FASTA was written to GCF_000344175.1_ASM34417v1_genomic.fna/markers.fasta
[2024-01-24 13:19:33,743] [INFO] Task started: Blastn
[2024-01-24 13:19:33,743] [INFO] Running command: blastn -query GCF_000344175.1_ASM34417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/reference_markers.fasta -out GCF_000344175.1_ASM34417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,396] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,400] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:34,400] [INFO] Target genome list was writen to GCF_000344175.1_ASM34417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:34,489] [INFO] Task started: fastANI
[2024-01-24 13:19:34,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd3eba6-f4a1-454c-86e2-b84325150058/GCF_000344175.1_ASM34417v1_genomic.fna.gz --refList GCF_000344175.1_ASM34417v1_genomic.fna/target_genomes.txt --output GCF_000344175.1_ASM34417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:42,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:42,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:42,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:42,016] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:19:42,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:42,017] [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 fleischmannii subsp. fleischmannii	strain=LU2006-1	GCA_000344175.1	1671902	1069827	type	True	100.0	899	902	95	conclusive
Listeria fleischmannii subsp. coloradonensis	strain=NCTC13938	GCA_900452975.1	1081736	1069827	type	True	95.874	847	902	95	conclusive
Listeria fleischmannii subsp. coloradonensis	strain=TTU M1-001	GCA_000252625.2	1081736	1069827	type	True	95.5165	673	902	95	conclusive
Listeria goaensis	strain=ILCC801	GCA_900186125.1	1649188	1649188	type	True	82.5688	617	902	95	below_threshold
Listeria floridensis	strain=FSL S10-1187	GCA_000525875.1	1494962	1494962	type	True	78.2857	219	902	95	below_threshold
Listeria aquatica	strain=FSL S10-1188	GCA_000525795.1	1494960	1494960	type	True	78.127	217	902	95	below_threshold
Listeria immobilis	strain=FSL L7-1519	GCA_014322765.1	2713502	2713502	type	True	77.911	185	902	95	below_threshold
Listeria ivanovii subsp. ivanovii	strain=PAM 55	GCA_000252975.1	202751	1638	claderef	True	77.8321	209	902	95	below_threshold
Listeria rocourtiae	strain=FSL F6-920	GCA_000525975.1	647910	647910	type	True	77.3726	124	902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,019] [INFO] DFAST Taxonomy check result was written to GCF_000344175.1_ASM34417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:42,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:42,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:42,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/checkm_data
[2024-01-24 13:19:42,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:42,053] [INFO] Task started: CheckM
[2024-01-24 13:19:42,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000344175.1_ASM34417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000344175.1_ASM34417v1_genomic.fna/checkm_input GCF_000344175.1_ASM34417v1_genomic.fna/checkm_result
[2024-01-24 13:20:05,599] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:05,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:05,622] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:05,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:05,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000344175.1_ASM34417v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:05,624] [INFO] Task started: Blastn
[2024-01-24 13:20:05,624] [INFO] Running command: blastn -query GCF_000344175.1_ASM34417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44375be-12c2-4b48-b9a3-34435a87bf2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000344175.1_ASM34417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:06,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:06,650] [INFO] Selected 16 target genomes.
[2024-01-24 13:20:06,650] [INFO] Target genome list was writen to GCF_000344175.1_ASM34417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:06,875] [INFO] Task started: fastANI
[2024-01-24 13:20:06,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd3eba6-f4a1-454c-86e2-b84325150058/GCF_000344175.1_ASM34417v1_genomic.fna.gz --refList GCF_000344175.1_ASM34417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000344175.1_ASM34417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:14,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:14,746] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:14,746] [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_000344175.1	s__Listeria fleischmannii	100.0	899	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	96.87	95.72	0.93	0.89	9	conclusive
GCF_900186125.1	s__Listeria goaensis	82.5979	615	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.59	99.37	0.97	0.94	8	-
GCF_000525875.1	s__Listeria floridensis	78.2857	219	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011800755.1	s__Listeria valentina	78.2129	201	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060285.1	s__Listeria welshimeri	78.1886	199	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.96	98.73	0.93	0.90	49	-
GCF_003369925.1	s__Listeria kieliensis_A	78.1752	218	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	99.04	0.93	0.93	2	-
GCF_000525795.1	s__Listeria aquatica	78.1059	217	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.71	97.71	0.93	0.93	2	-
GCF_000763495.1	s__Listeria londoniensis	78.0317	202	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.36	98.73	0.96	0.94	17	-
GCF_900183385.1	s__Listeria costaricensis	77.989	169	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014229645.1	s__Listeria sp014229645	77.9295	196	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014322765.1	s__Listeria immobilis	77.911	185	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	97.95	0.95	0.87	9	-
GCF_900187025.1	s__Listeria ivanovii	77.8882	204	902	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.75	99.44	0.99	0.97	26	-
GCF_013820765.1	s__Listeria_A rustica	77.5254	116	902	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	77.5179	120	902	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_000525975.1	s__Listeria_A rocourtiae	77.3726	124	902	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 13:20:14,748] [INFO] GTDB search result was written to GCF_000344175.1_ASM34417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:14,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:14,752] [INFO] DFAST_QC result json was written to GCF_000344175.1_ASM34417v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:14,752] [INFO] DFAST_QC completed!
[2024-01-24 13:20:14,752] [INFO] Total running time: 0h0m48s