[2023-06-12 22:40:45,432] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:40:45,436] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:40:45,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference
[2023-06-12 22:40:47,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:40:47,702] [INFO] Task started: Prodigal
[2023-06-12 22:40:47,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg87629fd8-2292-4341-995b-2b1c43173802/GCA_022483705.1_ASM2248370v1_genomic.fna.gz | prodigal -d GCA_022483705.1_ASM2248370v1_genomic.fna/cds.fna -a GCA_022483705.1_ASM2248370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:40:51,037] [INFO] Task succeeded: Prodigal
[2023-06-12 22:40:51,038] [INFO] Task started: HMMsearch
[2023-06-12 22:40:51,038] [INFO] Running command: hmmsearch --tblout GCA_022483705.1_ASM2248370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/reference_markers.hmm GCA_022483705.1_ASM2248370v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:40:51,292] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:40:51,294] [INFO] Found 6/6 markers.
[2023-06-12 22:40:51,314] [INFO] Query marker FASTA was written to GCA_022483705.1_ASM2248370v1_genomic.fna/markers.fasta
[2023-06-12 22:40:51,314] [INFO] Task started: Blastn
[2023-06-12 22:40:51,315] [INFO] Running command: blastn -query GCA_022483705.1_ASM2248370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/reference_markers.fasta -out GCA_022483705.1_ASM2248370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:40:52,718] [INFO] Task succeeded: Blastn
[2023-06-12 22:40:52,723] [INFO] Selected 17 target genomes.
[2023-06-12 22:40:52,724] [INFO] Target genome list was writen to GCA_022483705.1_ASM2248370v1_genomic.fna/target_genomes.txt
[2023-06-12 22:40:52,745] [INFO] Task started: fastANI
[2023-06-12 22:40:52,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg87629fd8-2292-4341-995b-2b1c43173802/GCA_022483705.1_ASM2248370v1_genomic.fna.gz --refList GCA_022483705.1_ASM2248370v1_genomic.fna/target_genomes.txt --output GCA_022483705.1_ASM2248370v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:40:58,673] [INFO] Task succeeded: fastANI
[2023-06-12 22:40:58,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:40:58,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:40:58,685] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-12 22:40:58,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-12 22:40:58,685] [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
Pediococcus pentosaceus	strain=FDAARGOS_1009	GCA_016127775.1	1255	1255	type	True	98.8659	509	547	95	conclusive
Pediococcus pentosaceus	strain=ATCC 33316	GCA_004354495.1	1255	1255	type	True	98.855	503	547	95	conclusive
Pediococcus pentosaceus	strain=DSM 20336	GCA_001437285.1	1255	1255	type	True	98.8276	501	547	95	conclusive
Pediococcus acidilactici	strain=CCUG 32235	GCA_012396515.1	1254	1254	neotype	True	79.9107	181	547	95	below_threshold
Pediococcus acidilactici	strain=DSM 20284	GCA_000146325.1	1254	1254	neotype	True	79.8297	186	547	95	below_threshold
Pediococcus argentinicus	strain=DSM 23026	GCA_001437605.1	480391	480391	type	True	78.5401	141	547	95	below_threshold
Pediococcus argentinicus	strain=CCUG 54535	GCA_012396535.1	480391	480391	type	True	78.4721	141	547	95	below_threshold
Pediococcus parvulus	strain=JCM 5889	GCA_014651215.1	54062	54062	type	True	77.4693	80	547	95	below_threshold
Pediococcus parvulus	strain=NBRC 100673	GCA_007990205.1	54062	54062	type	True	77.3463	79	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:40:58,687] [INFO] DFAST Taxonomy check result was written to GCA_022483705.1_ASM2248370v1_genomic.fna/tc_result.tsv
[2023-06-12 22:40:58,688] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:40:58,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:40:58,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/checkm_data
[2023-06-12 22:40:58,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:40:58,714] [INFO] Task started: CheckM
[2023-06-12 22:40:58,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022483705.1_ASM2248370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022483705.1_ASM2248370v1_genomic.fna/checkm_input GCA_022483705.1_ASM2248370v1_genomic.fna/checkm_result
[2023-06-12 22:41:16,853] [INFO] Task succeeded: CheckM
[2023-06-12 22:41:16,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:41:16,875] [INFO] ===== Completeness check finished =====
[2023-06-12 22:41:16,875] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:41:16,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022483705.1_ASM2248370v1_genomic.fna/markers.fasta)
[2023-06-12 22:41:16,876] [INFO] Task started: Blastn
[2023-06-12 22:41:16,876] [INFO] Running command: blastn -query GCA_022483705.1_ASM2248370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd4f873-3b20-4fcb-9a79-a429ecf6342d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022483705.1_ASM2248370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:17,602] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:17,607] [INFO] Selected 18 target genomes.
[2023-06-12 22:41:17,607] [INFO] Target genome list was writen to GCA_022483705.1_ASM2248370v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:41:17,617] [INFO] Task started: fastANI
[2023-06-12 22:41:17,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg87629fd8-2292-4341-995b-2b1c43173802/GCA_022483705.1_ASM2248370v1_genomic.fna.gz --refList GCA_022483705.1_ASM2248370v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022483705.1_ASM2248370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:41:25,661] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:25,671] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 22:41:25,672] [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_001437285.1	s__Pediococcus pentosaceus	98.8276	501	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.80	98.32	0.92	0.90	75	conclusive
GCF_001437075.1	s__Pediococcus stilesii	80.1484	236	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCA_009809575.1	s__Pediococcus acidilactici_A	79.922	181	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146325.1	s__Pediococcus acidilactici	79.8297	186	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.64	96.71	0.89	0.81	172	-
GCF_001437605.1	s__Pediococcus argentinicus	78.5401	141	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
GCF_001437255.1	s__Pediococcus damnosus	78.4942	63	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	-
GCF_001437405.1	s__Pediococcus ethanolidurans	78.2637	69	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.63	97.25	0.91	0.81	5	-
GCF_001438655.1	s__Pediococcus cellicola	77.6916	67	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000615845.1	s__Ligilactobacillus hayakitensis	77.515	52	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007990205.1	s__Pediococcus parvulus	77.3816	78	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-12 22:41:25,674] [INFO] GTDB search result was written to GCA_022483705.1_ASM2248370v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:41:25,674] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:41:25,678] [INFO] DFAST_QC result json was written to GCA_022483705.1_ASM2248370v1_genomic.fna/dqc_result.json
[2023-06-12 22:41:25,678] [INFO] DFAST_QC completed!
[2023-06-12 22:41:25,678] [INFO] Total running time: 0h0m40s