[2023-06-13 07:56:55,058] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:56:55,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:56:55,061] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference
[2023-06-13 07:56:57,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:56:57,109] [INFO] Task started: Prodigal
[2023-06-13 07:56:57,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg87939a41-6939-4eee-8a90-75d4fc2ed549/GCA_022641845.1_ASM2264184v1_genomic.fna.gz | prodigal -d GCA_022641845.1_ASM2264184v1_genomic.fna/cds.fna -a GCA_022641845.1_ASM2264184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:56:59,652] [INFO] Task succeeded: Prodigal
[2023-06-13 07:56:59,652] [INFO] Task started: HMMsearch
[2023-06-13 07:56:59,652] [INFO] Running command: hmmsearch --tblout GCA_022641845.1_ASM2264184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/reference_markers.hmm GCA_022641845.1_ASM2264184v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:56:59,867] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:56:59,868] [INFO] Found 6/6 markers.
[2023-06-13 07:56:59,887] [INFO] Query marker FASTA was written to GCA_022641845.1_ASM2264184v1_genomic.fna/markers.fasta
[2023-06-13 07:56:59,888] [INFO] Task started: Blastn
[2023-06-13 07:56:59,888] [INFO] Running command: blastn -query GCA_022641845.1_ASM2264184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/reference_markers.fasta -out GCA_022641845.1_ASM2264184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:57:01,595] [INFO] Task succeeded: Blastn
[2023-06-13 07:57:01,599] [INFO] Selected 12 target genomes.
[2023-06-13 07:57:01,600] [INFO] Target genome list was writen to GCA_022641845.1_ASM2264184v1_genomic.fna/target_genomes.txt
[2023-06-13 07:57:01,615] [INFO] Task started: fastANI
[2023-06-13 07:57:01,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg87939a41-6939-4eee-8a90-75d4fc2ed549/GCA_022641845.1_ASM2264184v1_genomic.fna.gz --refList GCA_022641845.1_ASM2264184v1_genomic.fna/target_genomes.txt --output GCA_022641845.1_ASM2264184v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:57:05,370] [INFO] Task succeeded: fastANI
[2023-06-13 07:57:05,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:57:05,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:57:05,383] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 07:57:05,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 07:57:05,384] [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	99.426	405	425	95	conclusive
Pediococcus pentosaceus	strain=DSM 20336	GCA_001437285.1	1255	1255	type	True	99.3797	402	425	95	conclusive
Pediococcus pentosaceus	strain=ATCC 33316	GCA_004354495.1	1255	1255	type	True	99.324	407	425	95	conclusive
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	79.9701	51	425	95	below_threshold
Pediococcus acidilactici	strain=CCUG 32235	GCA_012396515.1	1254	1254	neotype	True	79.9276	160	425	95	below_threshold
Pediococcus acidilactici	strain=DSM 20284	GCA_000146325.1	1254	1254	neotype	True	79.8291	160	425	95	below_threshold
Pediococcus argentinicus	strain=DSM 23026	GCA_001437605.1	480391	480391	type	True	78.96	111	425	95	below_threshold
Pediococcus argentinicus	strain=CCUG 54535	GCA_012396535.1	480391	480391	type	True	78.9548	111	425	95	below_threshold
Pediococcus parvulus	strain=JCM 5889	GCA_014651215.1	54062	54062	type	True	77.6458	64	425	95	below_threshold
Pediococcus parvulus	strain=NBRC 100673	GCA_007990205.1	54062	54062	type	True	77.4342	61	425	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:57:05,386] [INFO] DFAST Taxonomy check result was written to GCA_022641845.1_ASM2264184v1_genomic.fna/tc_result.tsv
[2023-06-13 07:57:05,386] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:57:05,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:57:05,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/checkm_data
[2023-06-13 07:57:05,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:57:05,404] [INFO] Task started: CheckM
[2023-06-13 07:57:05,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022641845.1_ASM2264184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022641845.1_ASM2264184v1_genomic.fna/checkm_input GCA_022641845.1_ASM2264184v1_genomic.fna/checkm_result
[2023-06-13 07:57:21,189] [INFO] Task succeeded: CheckM
[2023-06-13 07:57:21,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:57:21,209] [INFO] ===== Completeness check finished =====
[2023-06-13 07:57:21,209] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:57:21,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022641845.1_ASM2264184v1_genomic.fna/markers.fasta)
[2023-06-13 07:57:21,210] [INFO] Task started: Blastn
[2023-06-13 07:57:21,210] [INFO] Running command: blastn -query GCA_022641845.1_ASM2264184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb2aae2a-dfd2-4e34-a154-e77f767a4ee0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022641845.1_ASM2264184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:57:22,158] [INFO] Task succeeded: Blastn
[2023-06-13 07:57:22,162] [INFO] Selected 18 target genomes.
[2023-06-13 07:57:22,162] [INFO] Target genome list was writen to GCA_022641845.1_ASM2264184v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:57:22,171] [INFO] Task started: fastANI
[2023-06-13 07:57:22,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg87939a41-6939-4eee-8a90-75d4fc2ed549/GCA_022641845.1_ASM2264184v1_genomic.fna.gz --refList GCA_022641845.1_ASM2264184v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022641845.1_ASM2264184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:57:28,747] [INFO] Task succeeded: fastANI
[2023-06-13 07:57:28,756] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:57:28,756] [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	99.3797	402	425	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	80.5927	207	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCF_014058425.1	s__Companilactobacillus pabuli	79.9701	51	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCA_009809575.1	s__Pediococcus acidilactici_A	79.9015	156	425	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	79.8291	160	425	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	79.0007	110	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
GCF_001437405.1	s__Pediococcus ethanolidurans	77.7902	67	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.63	97.25	0.91	0.81	5	-
GCF_007990205.1	s__Pediococcus parvulus	77.4342	61	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
GCF_001437255.1	s__Pediococcus damnosus	77.4244	60	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	-
GCF_001438655.1	s__Pediococcus cellicola	77.4141	60	425	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 07:57:28,758] [INFO] GTDB search result was written to GCA_022641845.1_ASM2264184v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:57:28,759] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:57:28,762] [INFO] DFAST_QC result json was written to GCA_022641845.1_ASM2264184v1_genomic.fna/dqc_result.json
[2023-06-13 07:57:28,762] [INFO] DFAST_QC completed!
[2023-06-13 07:57:28,763] [INFO] Total running time: 0h0m34s