[2024-01-24 10:47:06,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,545] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,106] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgdca1fab9-657a-4b54-96da-dd65840b3758/GCF_016861655.1_ASM1686165v1_genomic.fna.gz | prodigal -d GCF_016861655.1_ASM1686165v1_genomic.fna/cds.fna -a GCF_016861655.1_ASM1686165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:19,800] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:19,801] [INFO] Task started: HMMsearch
[2024-01-24 10:47:19,801] [INFO] Running command: hmmsearch --tblout GCF_016861655.1_ASM1686165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/reference_markers.hmm GCF_016861655.1_ASM1686165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,060] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,082] [INFO] Query marker FASTA was written to GCF_016861655.1_ASM1686165v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,083] [INFO] Task started: Blastn
[2024-01-24 10:47:20,083] [INFO] Running command: blastn -query GCF_016861655.1_ASM1686165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/reference_markers.fasta -out GCF_016861655.1_ASM1686165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:20,690] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:20,693] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:20,694] [INFO] Target genome list was writen to GCF_016861655.1_ASM1686165v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,699] [INFO] Task started: fastANI
[2024-01-24 10:47:20,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca1fab9-657a-4b54-96da-dd65840b3758/GCF_016861655.1_ASM1686165v1_genomic.fna.gz --refList GCF_016861655.1_ASM1686165v1_genomic.fna/target_genomes.txt --output GCF_016861655.1_ASM1686165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:29,731] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:29,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:29,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:29,740] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:29,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:29,741] [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 lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	100.0	996	996	95	conclusive
Levilactobacillus wangkuiensis	strain=6-5(1)	GCA_016861605.1	2799566	2799566	type	True	93.7659	887	996	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	93.1106	880	996	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	83.9594	696	996	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	82.9533	585	996	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	82.7378	605	996	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	82.0626	511	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:29,743] [INFO] DFAST Taxonomy check result was written to GCF_016861655.1_ASM1686165v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:29,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:29,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:29,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/checkm_data
[2024-01-24 10:47:29,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:29,790] [INFO] Task started: CheckM
[2024-01-24 10:47:29,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861655.1_ASM1686165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861655.1_ASM1686165v1_genomic.fna/checkm_input GCF_016861655.1_ASM1686165v1_genomic.fna/checkm_result
[2024-01-24 10:47:59,574] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:59,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,598] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:59,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:59,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861655.1_ASM1686165v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:59,599] [INFO] Task started: Blastn
[2024-01-24 10:47:59,599] [INFO] Running command: blastn -query GCF_016861655.1_ASM1686165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfcca95a-f30d-4e4c-a277-b914632d8332/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861655.1_ASM1686165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:00,419] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:00,424] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:00,424] [INFO] Target genome list was writen to GCF_016861655.1_ASM1686165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:00,457] [INFO] Task started: fastANI
[2024-01-24 10:48:00,457] [INFO] Running command: fastANI --query /var/lib/cwl/stgdca1fab9-657a-4b54-96da-dd65840b3758/GCF_016861655.1_ASM1686165v1_genomic.fna.gz --refList GCF_016861655.1_ASM1686165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861655.1_ASM1686165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:09,122] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,130] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:09,130] [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_016861655.1	s__Levilactobacillus sp016861655	100.0	996	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	conclusive
GCF_016861585.1	s__Levilactobacillus sp016861585	93.7212	893	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_003946045.1	s__Levilactobacillus mulengensis	93.1106	880	996	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	83.9865	694	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946085.1	s__Levilactobacillus angrenensis	82.9423	586	996	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	82.7554	604	996	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	82.6914	626	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861695.1	s__Levilactobacillus sp016861695	82.0591	511	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,133] [INFO] GTDB search result was written to GCF_016861655.1_ASM1686165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:09,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:09,136] [INFO] DFAST_QC result json was written to GCF_016861655.1_ASM1686165v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:09,136] [INFO] DFAST_QC completed!
[2024-01-24 10:48:09,136] [INFO] Total running time: 0h1m3s