[2024-01-24 13:22:10,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference
[2024-01-24 13:22:12,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:12,096] [INFO] Task started: Prodigal
[2024-01-24 13:22:12,097] [INFO] Running command: gunzip -c /var/lib/cwl/stga929d9ad-3207-4635-83e2-2032f2859e12/GCF_003641185.1_ASM364118v1_genomic.fna.gz | prodigal -d GCF_003641185.1_ASM364118v1_genomic.fna/cds.fna -a GCF_003641185.1_ASM364118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:21,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:21,376] [INFO] Task started: HMMsearch
[2024-01-24 13:22:21,376] [INFO] Running command: hmmsearch --tblout GCF_003641185.1_ASM364118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/reference_markers.hmm GCF_003641185.1_ASM364118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:21,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:21,635] [INFO] Found 6/6 markers.
[2024-01-24 13:22:21,666] [INFO] Query marker FASTA was written to GCF_003641185.1_ASM364118v1_genomic.fna/markers.fasta
[2024-01-24 13:22:21,667] [INFO] Task started: Blastn
[2024-01-24 13:22:21,667] [INFO] Running command: blastn -query GCF_003641185.1_ASM364118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/reference_markers.fasta -out GCF_003641185.1_ASM364118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:22,297] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:22,300] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:22,301] [INFO] Target genome list was writen to GCF_003641185.1_ASM364118v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:22,307] [INFO] Task started: fastANI
[2024-01-24 13:22:22,308] [INFO] Running command: fastANI --query /var/lib/cwl/stga929d9ad-3207-4635-83e2-2032f2859e12/GCF_003641185.1_ASM364118v1_genomic.fna.gz --refList GCF_003641185.1_ASM364118v1_genomic.fna/target_genomes.txt --output GCF_003641185.1_ASM364118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:37,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:37,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:37,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:37,580] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:37,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:37,580] [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
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	100.0	1223	1223	95	conclusive
Lactiplantibacillus pentosus	strain=ATCC 8041	GCA_004354685.1	1589	1589	type	True	99.9802	1205	1223	95	conclusive
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	99.9413	1185	1223	95	conclusive
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	83.006	703	1223	95	below_threshold
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	82.7299	671	1223	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	82.7148	667	1223	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	82.5835	656	1223	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	79.1912	74	1223	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	78.4756	66	1223	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.8156	70	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:37,582] [INFO] DFAST Taxonomy check result was written to GCF_003641185.1_ASM364118v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:37,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:37,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:37,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/checkm_data
[2024-01-24 13:22:37,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:37,640] [INFO] Task started: CheckM
[2024-01-24 13:22:37,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003641185.1_ASM364118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003641185.1_ASM364118v1_genomic.fna/checkm_input GCF_003641185.1_ASM364118v1_genomic.fna/checkm_result
[2024-01-24 13:23:13,067] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:13,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:13,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:13,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003641185.1_ASM364118v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:13,090] [INFO] Task started: Blastn
[2024-01-24 13:23:13,090] [INFO] Running command: blastn -query GCF_003641185.1_ASM364118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37a1c45c-c65f-4ae6-b243-11899ae9658b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003641185.1_ASM364118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:13,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:13,936] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:13,936] [INFO] Target genome list was writen to GCF_003641185.1_ASM364118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:13,944] [INFO] Task started: fastANI
[2024-01-24 13:23:13,944] [INFO] Running command: fastANI --query /var/lib/cwl/stga929d9ad-3207-4635-83e2-2032f2859e12/GCF_003641185.1_ASM364118v1_genomic.fna.gz --refList GCF_003641185.1_ASM364118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003641185.1_ASM364118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:25,877] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:25,893] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:25,893] [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_003641185.1	s__Lactiplantibacillus pentosus	100.0	1223	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	conclusive
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	93.2748	1017	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_014131735.1	s__Lactiplantibacillus plantarum	82.7718	668	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_003641145.1	s__Lactiplantibacillus paraplantarum	82.609	658	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.7823	399	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.6434	394	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039045.1	s__Lactiplantibacillus herbarum	80.4924	454	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.2309	382	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.924	330	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	79.8273	327	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:25,895] [INFO] GTDB search result was written to GCF_003641185.1_ASM364118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:25,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:25,899] [INFO] DFAST_QC result json was written to GCF_003641185.1_ASM364118v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:25,900] [INFO] DFAST_QC completed!
[2024-01-24 13:23:25,900] [INFO] Total running time: 0h1m15s