[2024-01-24 13:32:16,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,176] [INFO] DQC Reference Directory: /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference
[2024-01-24 13:32:17,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:17,510] [INFO] Task started: Prodigal
[2024-01-24 13:32:17,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg4181e5c9-983c-41a1-8485-344d7824a821/GCF_004354735.1_ASM435473v1_genomic.fna.gz | prodigal -d GCF_004354735.1_ASM435473v1_genomic.fna/cds.fna -a GCF_004354735.1_ASM435473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:22,389] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:22,390] [INFO] Task started: HMMsearch
[2024-01-24 13:32:22,390] [INFO] Running command: hmmsearch --tblout GCF_004354735.1_ASM435473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/reference_markers.hmm GCF_004354735.1_ASM435473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:22,647] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:22,649] [INFO] Found 6/6 markers.
[2024-01-24 13:32:22,672] [INFO] Query marker FASTA was written to GCF_004354735.1_ASM435473v1_genomic.fna/markers.fasta
[2024-01-24 13:32:22,673] [INFO] Task started: Blastn
[2024-01-24 13:32:22,673] [INFO] Running command: blastn -query GCF_004354735.1_ASM435473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/reference_markers.fasta -out GCF_004354735.1_ASM435473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:23,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:23,328] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:23,328] [INFO] Target genome list was writen to GCF_004354735.1_ASM435473v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:23,340] [INFO] Task started: fastANI
[2024-01-24 13:32:23,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg4181e5c9-983c-41a1-8485-344d7824a821/GCF_004354735.1_ASM435473v1_genomic.fna.gz --refList GCF_004354735.1_ASM435473v1_genomic.fna/target_genomes.txt --output GCF_004354735.1_ASM435473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:27,898] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:27,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:27,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:27,906] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:27,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:27,906] [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
Secundilactobacillus malefermentans	strain=ATCC 49373	GCA_004354735.1	176292	176292	type	True	100.0	680	684	95	conclusive
Secundilactobacillus malefermentans	strain=DSM 5705	GCA_001436395.1	176292	176292	type	True	99.858	596	684	95	conclusive
Secundilactobacillus malefermentans	strain=KCTC 3548	GCA_000260775.1	176292	176292	type	True	99.8278	582	684	95	conclusive
Secundilactobacillus oryzae	strain=SG293	GCA_000740055.1	1202668	1202668	type	True	79.6661	213	684	95	below_threshold
Secundilactobacillus oryzae	strain=JCM 18671	GCA_001311525.1	1202668	1202668	type	True	79.52	211	684	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	77.9439	67	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:27,908] [INFO] DFAST Taxonomy check result was written to GCF_004354735.1_ASM435473v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:27,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:27,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:27,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/checkm_data
[2024-01-24 13:32:27,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:27,938] [INFO] Task started: CheckM
[2024-01-24 13:32:27,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354735.1_ASM435473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354735.1_ASM435473v1_genomic.fna/checkm_input GCF_004354735.1_ASM435473v1_genomic.fna/checkm_result
[2024-01-24 13:32:50,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:50,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:50,361] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:50,362] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:50,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354735.1_ASM435473v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:50,363] [INFO] Task started: Blastn
[2024-01-24 13:32:50,363] [INFO] Running command: blastn -query GCF_004354735.1_ASM435473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga36c407e-0823-4aa4-9ea7-3ba545cadc74/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354735.1_ASM435473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,124] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:51,124] [INFO] Target genome list was writen to GCF_004354735.1_ASM435473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:51,134] [INFO] Task started: fastANI
[2024-01-24 13:32:51,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg4181e5c9-983c-41a1-8485-344d7824a821/GCF_004354735.1_ASM435473v1_genomic.fna.gz --refList GCF_004354735.1_ASM435473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354735.1_ASM435473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:00,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,515] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:00,516] [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_001436395.1	s__Secundilactobacillus malefermentans	99.858	596	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.75	99.27	0.97	0.94	4	conclusive
GCF_003946265.1	s__Levilactobacillus yonginensis	80.734	70	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434255.1	s__Lentilactobacillus diolivorans	80.417	62	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.05	98.10	0.95	0.90	3	-
GCF_003946095.1	s__Levilactobacillus lindianensis	80.1336	55	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	79.6743	63	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740055.1	s__Secundilactobacillus oryzae	79.6661	213	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_002583405.1	s__Secundilactobacillus silagincola	79.5288	72	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_001435975.1	s__Secundilactobacillus collinoides	79.4529	68	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.82	99.79	0.97	0.94	3	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	79.1033	74	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990205.1	s__Pediococcus parvulus	78.3514	53	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.29	98.77	0.93	0.88	4	-
GCF_016861565.1	s__Secundilactobacillus sp016861565	77.8539	70	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,518] [INFO] GTDB search result was written to GCF_004354735.1_ASM435473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:00,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:00,522] [INFO] DFAST_QC result json was written to GCF_004354735.1_ASM435473v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:00,523] [INFO] DFAST_QC completed!
[2024-01-24 13:33:00,523] [INFO] Total running time: 0h0m44s