[2024-01-24 12:29:28,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference
[2024-01-24 12:29:30,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,244] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg45f99961-3b9a-4f57-b8f5-e872e770fc40/GCF_001592085.1_ASM159208v1_genomic.fna.gz | prodigal -d GCF_001592085.1_ASM159208v1_genomic.fna/cds.fna -a GCF_001592085.1_ASM159208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:35,625] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:35,625] [INFO] Task started: HMMsearch
[2024-01-24 12:29:35,625] [INFO] Running command: hmmsearch --tblout GCF_001592085.1_ASM159208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/reference_markers.hmm GCF_001592085.1_ASM159208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:35,943] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:35,944] [INFO] Found 6/6 markers.
[2024-01-24 12:29:35,987] [INFO] Query marker FASTA was written to GCF_001592085.1_ASM159208v1_genomic.fna/markers.fasta
[2024-01-24 12:29:35,988] [INFO] Task started: Blastn
[2024-01-24 12:29:35,988] [INFO] Running command: blastn -query GCF_001592085.1_ASM159208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/reference_markers.fasta -out GCF_001592085.1_ASM159208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:36,617] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:36,621] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:36,621] [INFO] Target genome list was writen to GCF_001592085.1_ASM159208v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:36,630] [INFO] Task started: fastANI
[2024-01-24 12:29:36,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f99961-3b9a-4f57-b8f5-e872e770fc40/GCF_001592085.1_ASM159208v1_genomic.fna.gz --refList GCF_001592085.1_ASM159208v1_genomic.fna/target_genomes.txt --output GCF_001592085.1_ASM159208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:45,390] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:45,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:45,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:45,401] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:45,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:45,401] [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
Levilactobacillus senmaizukei	strain=NBRC 103853	GCA_001592085.1	431273	431273	type	True	100.0	694	699	95	conclusive
Levilactobacillus senmaizukei	strain=DSM 21775	GCA_001436675.1	431273	431273	type	True	99.9985	695	699	95	conclusive
Levilactobacillus tangyuanensis	strain=137-3	GCA_003946545.1	2486021	2486021	type	True	87.8694	607	699	95	below_threshold
Levilactobacillus tongjiangensis	strain=218-10	GCA_003946345.1	2486023	2486023	type	True	80.4803	290	699	95	below_threshold
Levilactobacillus fujinensis	strain=218-6	GCA_003946335.1	2486024	2486024	type	True	80.4244	258	699	95	below_threshold
Levilactobacillus yonginensis	strain=JCM 18023	GCA_003946265.1	1054041	1054041	type	True	80.3466	306	699	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	80.0758	279	699	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	80.0671	286	699	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	80.0109	318	699	95	below_threshold
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	79.916	286	699	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	79.7285	255	699	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	78.1911	63	699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:45,403] [INFO] DFAST Taxonomy check result was written to GCF_001592085.1_ASM159208v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:45,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:45,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:45,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/checkm_data
[2024-01-24 12:29:45,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:45,434] [INFO] Task started: CheckM
[2024-01-24 12:29:45,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592085.1_ASM159208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592085.1_ASM159208v1_genomic.fna/checkm_input GCF_001592085.1_ASM159208v1_genomic.fna/checkm_result
[2024-01-24 12:30:09,427] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:09,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,447] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:09,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:09,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592085.1_ASM159208v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:09,448] [INFO] Task started: Blastn
[2024-01-24 12:30:09,449] [INFO] Running command: blastn -query GCF_001592085.1_ASM159208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18bd8ed6-546b-473d-95fe-2beb54b5a0a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592085.1_ASM159208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:10,270] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:10,273] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:10,274] [INFO] Target genome list was writen to GCF_001592085.1_ASM159208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:10,285] [INFO] Task started: fastANI
[2024-01-24 12:30:10,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f99961-3b9a-4f57-b8f5-e872e770fc40/GCF_001592085.1_ASM159208v1_genomic.fna.gz --refList GCF_001592085.1_ASM159208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592085.1_ASM159208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:20,417] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:20,430] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:20,431] [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_001592085.1	s__Levilactobacillus senmaizukei	100.0	694	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003946545.1	s__Levilactobacillus tangyuanensis	87.8914	606	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946345.1	s__Levilactobacillus tongjiangensis	80.4803	290	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946335.1	s__Levilactobacillus fujinensis	80.4244	258	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	80.4095	284	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666485.1	s__Levilactobacillus brevis_A	80.4076	292	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	80.3113	290	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946265.1	s__Levilactobacillus yonginensis	80.3088	308	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	80.0958	278	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861585.1	s__Levilactobacillus sp016861585	80.07	318	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_003946085.1	s__Levilactobacillus angrenensis	80.0671	286	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861655.1	s__Levilactobacillus sp016861655	79.9934	319	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_001434395.1	s__Levilactobacillus hammesii	79.897	287	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641185.1	s__Levilactobacillus sp012641185	79.7285	255	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	-
GCF_001435095.1	s__Levilactobacillus spicheri	79.4534	199	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:20,432] [INFO] GTDB search result was written to GCF_001592085.1_ASM159208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:20,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:20,437] [INFO] DFAST_QC result json was written to GCF_001592085.1_ASM159208v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:20,438] [INFO] DFAST_QC completed!
[2024-01-24 12:30:20,438] [INFO] Total running time: 0h0m52s