[2024-01-25 17:49:20,346] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:20,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:20,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference
[2024-01-25 17:49:21,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:21,509] [INFO] Task started: Prodigal
[2024-01-25 17:49:21,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bcdebd4-f156-4c4d-86f0-5387638cc708/GCF_000159435.1_ASM15943v1_genomic.fna.gz | prodigal -d GCF_000159435.1_ASM15943v1_genomic.fna/cds.fna -a GCF_000159435.1_ASM15943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:24,836] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:24,836] [INFO] Task started: HMMsearch
[2024-01-25 17:49:24,836] [INFO] Running command: hmmsearch --tblout GCF_000159435.1_ASM15943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/reference_markers.hmm GCF_000159435.1_ASM15943v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:25,023] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:25,024] [INFO] Found 6/6 markers.
[2024-01-25 17:49:25,044] [INFO] Query marker FASTA was written to GCF_000159435.1_ASM15943v1_genomic.fna/markers.fasta
[2024-01-25 17:49:25,044] [INFO] Task started: Blastn
[2024-01-25 17:49:25,044] [INFO] Running command: blastn -query GCF_000159435.1_ASM15943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/reference_markers.fasta -out GCF_000159435.1_ASM15943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:25,605] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:25,607] [INFO] Selected 10 target genomes.
[2024-01-25 17:49:25,607] [INFO] Target genome list was writen to GCF_000159435.1_ASM15943v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:25,618] [INFO] Task started: fastANI
[2024-01-25 17:49:25,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bcdebd4-f156-4c4d-86f0-5387638cc708/GCF_000159435.1_ASM15943v1_genomic.fna.gz --refList GCF_000159435.1_ASM15943v1_genomic.fna/target_genomes.txt --output GCF_000159435.1_ASM15943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:30,086] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:30,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:30,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:30,093] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:49:30,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:30,093] [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
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	99.9995	603	608	95	conclusive
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	99.871	519	608	95	conclusive
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	91.5468	509	608	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	90.9007	494	608	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	84.2412	404	608	95	below_threshold
Limosilactobacillus frumenti	strain=DSM 13145	GCA_001436045.1	104955	104955	type	True	79.9505	215	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:30,094] [INFO] DFAST Taxonomy check result was written to GCF_000159435.1_ASM15943v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:30,096] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:30,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:30,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/checkm_data
[2024-01-25 17:49:30,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:30,117] [INFO] Task started: CheckM
[2024-01-25 17:49:30,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159435.1_ASM15943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159435.1_ASM15943v1_genomic.fna/checkm_input GCF_000159435.1_ASM15943v1_genomic.fna/checkm_result
[2024-01-25 17:49:46,297] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:46,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:46,309] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:46,310] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:46,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159435.1_ASM15943v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:46,310] [INFO] Task started: Blastn
[2024-01-25 17:49:46,310] [INFO] Running command: blastn -query GCF_000159435.1_ASM15943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50eeafa3-cbe9-4371-8769-76b696655f0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159435.1_ASM15943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:47,062] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:47,065] [INFO] Selected 8 target genomes.
[2024-01-25 17:49:47,065] [INFO] Target genome list was writen to GCF_000159435.1_ASM15943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:47,070] [INFO] Task started: fastANI
[2024-01-25 17:49:47,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bcdebd4-f156-4c4d-86f0-5387638cc708/GCF_000159435.1_ASM15943v1_genomic.fna.gz --refList GCF_000159435.1_ASM15943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159435.1_ASM15943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:50,534] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:50,540] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:50,540] [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_000159435.1	s__Limosilactobacillus vaginalis	99.9995	603	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.80	96.39	0.94	0.86	8	conclusive
GCF_014838735.1	s__Limosilactobacillus portuensis	91.5453	509	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.50	97.46	0.87	0.84	6	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	90.8894	494	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_014836425.1	s__Limosilactobacillus sp014836425	84.2637	403	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145505.1	s__Limosilactobacillus fastidiosus	82.6964	361	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	-
GCA_018883805.1	s__Limosilactobacillus merdavium	82.2875	286	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.07	96.07	0.81	0.81	2	-
GCF_001436045.1	s__Limosilactobacillus frumenti	79.9006	214	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.86	99.72	0.98	0.96	3	-
GCA_019117445.1	s__Limosilactobacillus excrementigallinarum	78.224	88	608	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.52	96.52	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:50,544] [INFO] GTDB search result was written to GCF_000159435.1_ASM15943v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:50,544] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:50,547] [INFO] DFAST_QC result json was written to GCF_000159435.1_ASM15943v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:50,547] [INFO] DFAST_QC completed!
[2024-01-25 17:49:50,547] [INFO] Total running time: 0h0m30s