[2024-01-24 14:46:35,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference
[2024-01-24 14:46:37,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,182] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,182] [INFO] Running command: gunzip -c /var/lib/cwl/stge9153e5e-5d7f-4fc5-94ee-18c8badc78d7/GCF_012396535.1_ASM1239653v1_genomic.fna.gz | prodigal -d GCF_012396535.1_ASM1239653v1_genomic.fna/cds.fna -a GCF_012396535.1_ASM1239653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:40,386] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:40,386] [INFO] Task started: HMMsearch
[2024-01-24 14:46:40,387] [INFO] Running command: hmmsearch --tblout GCF_012396535.1_ASM1239653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/reference_markers.hmm GCF_012396535.1_ASM1239653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:40,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:40,557] [INFO] Found 6/6 markers.
[2024-01-24 14:46:40,574] [INFO] Query marker FASTA was written to GCF_012396535.1_ASM1239653v1_genomic.fna/markers.fasta
[2024-01-24 14:46:40,575] [INFO] Task started: Blastn
[2024-01-24 14:46:40,575] [INFO] Running command: blastn -query GCF_012396535.1_ASM1239653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/reference_markers.fasta -out GCF_012396535.1_ASM1239653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:42,382] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:42,386] [INFO] Selected 23 target genomes.
[2024-01-24 14:46:42,386] [INFO] Target genome list was writen to GCF_012396535.1_ASM1239653v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:42,740] [INFO] Task started: fastANI
[2024-01-24 14:46:42,741] [INFO] Running command: fastANI --query /var/lib/cwl/stge9153e5e-5d7f-4fc5-94ee-18c8badc78d7/GCF_012396535.1_ASM1239653v1_genomic.fna.gz --refList GCF_012396535.1_ASM1239653v1_genomic.fna/target_genomes.txt --output GCF_012396535.1_ASM1239653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:49,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:49,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:49,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:49,145] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:46:49,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:46:49,145] [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 argentinicus	strain=CCUG 54535	GCA_012396535.1	480391	480391	type	True	100.0	547	549	95	conclusive
Pediococcus argentinicus	strain=DSM 23026	GCA_001437605.1	480391	480391	type	True	99.9273	520	549	95	conclusive
Pediococcus acidilactici	strain=CCUG 32235	GCA_012396515.1	1254	1254	neotype	True	79.6969	70	549	95	below_threshold
Pediococcus acidilactici	strain=FDAARGOS_1133	GCA_016726765.1	1254	1254	neotype	True	79.5348	72	549	95	below_threshold
Pediococcus acidilactici	strain=DSM 20284	GCA_000146325.1	1254	1254	neotype	True	79.2995	68	549	95	below_threshold
Pediococcus claussenii	strain=ATCC BAA-344	GCA_000237995.2	187452	187452	type	True	78.8408	116	549	95	below_threshold
Pediococcus claussenii	strain=DSM 14800	GCA_001436905.1	187452	187452	type	True	78.8008	116	549	95	below_threshold
Pediococcus pentosaceus	strain=ATCC 33316	GCA_004354495.1	1255	1255	type	True	78.6209	129	549	95	below_threshold
Pediococcus pentosaceus	strain=FDAARGOS_1009	GCA_016127775.1	1255	1255	type	True	78.6202	128	549	95	below_threshold
Pediococcus pentosaceus	strain=DSM 20336	GCA_001437285.1	1255	1255	type	True	78.4628	123	549	95	below_threshold
Pediococcus ethanolidurans	strain=DSM 22301	GCA_001437405.1	319653	319653	type	True	77.7974	99	549	95	below_threshold
Pediococcus cellicola	strain=DSM 17757	GCA_001438655.1	319652	319652	type	True	77.7594	79	549	95	below_threshold
Pediococcus ethanolidurans	strain=CGMCC 1.3889	GCA_900111205.1	319653	319653	type	True	77.5982	101	549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:49,148] [INFO] DFAST Taxonomy check result was written to GCF_012396535.1_ASM1239653v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:49,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:49,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:49,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/checkm_data
[2024-01-24 14:46:49,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:49,170] [INFO] Task started: CheckM
[2024-01-24 14:46:49,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396535.1_ASM1239653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396535.1_ASM1239653v1_genomic.fna/checkm_input GCF_012396535.1_ASM1239653v1_genomic.fna/checkm_result
[2024-01-24 14:47:08,241] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:08,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:08,259] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:08,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:08,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396535.1_ASM1239653v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:08,259] [INFO] Task started: Blastn
[2024-01-24 14:47:08,259] [INFO] Running command: blastn -query GCF_012396535.1_ASM1239653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074fa853-da1f-4489-9fdd-75e26080ce67/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396535.1_ASM1239653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:09,039] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:09,042] [INFO] Selected 24 target genomes.
[2024-01-24 14:47:09,042] [INFO] Target genome list was writen to GCF_012396535.1_ASM1239653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:09,060] [INFO] Task started: fastANI
[2024-01-24 14:47:09,060] [INFO] Running command: fastANI --query /var/lib/cwl/stge9153e5e-5d7f-4fc5-94ee-18c8badc78d7/GCF_012396535.1_ASM1239653v1_genomic.fna.gz --refList GCF_012396535.1_ASM1239653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396535.1_ASM1239653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:16,957] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:16,967] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:16,967] [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_001437605.1	s__Pediococcus argentinicus	99.9273	520	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	conclusive
GCF_000146325.1	s__Pediococcus acidilactici	79.2995	68	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.64	96.71	0.89	0.81	172	-
GCA_009809575.1	s__Pediococcus acidilactici_A	78.9756	85	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000237995.1	s__Pediococcus claussenii	78.8235	117	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.87	99.79	0.97	0.95	4	-
GCF_001437285.1	s__Pediococcus pentosaceus	78.4628	123	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.80	98.32	0.92	0.90	75	-
GCF_002982135.1	s__Pediococcus inopinatus	78.3651	86	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.47	98.95	0.96	0.92	3	-
GCF_001437075.1	s__Pediococcus stilesii	78.2579	116	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCF_007990205.1	s__Pediococcus parvulus	77.9328	78	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
GCF_001437405.1	s__Pediococcus ethanolidurans	77.8301	98	549	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	77.7594	79	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001437255.1	s__Pediococcus damnosus	77.6595	81	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.57	99.19	0.93	0.88	12	-
GCF_001435445.1	s__Companilactobacillus kimchii	76.86	51	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:16,969] [INFO] GTDB search result was written to GCF_012396535.1_ASM1239653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:16,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:16,972] [INFO] DFAST_QC result json was written to GCF_012396535.1_ASM1239653v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:16,972] [INFO] DFAST_QC completed!
[2024-01-24 14:47:16,972] [INFO] Total running time: 0h0m42s