[2024-01-24 14:14:46,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:46,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:46,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference
[2024-01-24 14:14:49,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,425] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe32fb82-9346-4631-81b0-3a7da3e524a6/GCF_001436045.1_ASM143604v1_genomic.fna.gz | prodigal -d GCF_001436045.1_ASM143604v1_genomic.fna/cds.fna -a GCF_001436045.1_ASM143604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:53,877] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:53,877] [INFO] Task started: HMMsearch
[2024-01-24 14:14:53,877] [INFO] Running command: hmmsearch --tblout GCF_001436045.1_ASM143604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/reference_markers.hmm GCF_001436045.1_ASM143604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:54,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:54,309] [INFO] Found 6/6 markers.
[2024-01-24 14:14:54,331] [INFO] Query marker FASTA was written to GCF_001436045.1_ASM143604v1_genomic.fna/markers.fasta
[2024-01-24 14:14:54,332] [INFO] Task started: Blastn
[2024-01-24 14:14:54,332] [INFO] Running command: blastn -query GCF_001436045.1_ASM143604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/reference_markers.fasta -out GCF_001436045.1_ASM143604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:57,104] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:57,108] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:57,109] [INFO] Target genome list was writen to GCF_001436045.1_ASM143604v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:57,330] [INFO] Task started: fastANI
[2024-01-24 14:14:57,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe32fb82-9346-4631-81b0-3a7da3e524a6/GCF_001436045.1_ASM143604v1_genomic.fna.gz --refList GCF_001436045.1_ASM143604v1_genomic.fna/target_genomes.txt --output GCF_001436045.1_ASM143604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:04,283] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:04,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:04,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:04,299] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:04,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:04,300] [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 frumenti	strain=DSM 13145	GCA_001436045.1	104955	104955	type	True	100.0	565	567	95	conclusive
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	80.0593	210	567	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	79.9374	206	567	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	79.8423	199	567	95	below_threshold
Limosilactobacillus fastidiosus	strain=WF-MO7-1	GCA_014145505.1	2759855	2759855	type	True	79.8179	183	567	95	below_threshold
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	79.7536	188	567	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	79.7471	189	567	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	79.0784	159	567	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	79.0075	158	567	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	78.9342	152	567	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	78.6567	153	567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:04,301] [INFO] DFAST Taxonomy check result was written to GCF_001436045.1_ASM143604v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:04,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:04,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:04,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/checkm_data
[2024-01-24 14:15:04,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:04,326] [INFO] Task started: CheckM
[2024-01-24 14:15:04,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436045.1_ASM143604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436045.1_ASM143604v1_genomic.fna/checkm_input GCF_001436045.1_ASM143604v1_genomic.fna/checkm_result
[2024-01-24 14:15:24,669] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:24,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:24,687] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:24,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:24,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436045.1_ASM143604v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:24,688] [INFO] Task started: Blastn
[2024-01-24 14:15:24,688] [INFO] Running command: blastn -query GCF_001436045.1_ASM143604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897b281d-d5c6-4e6a-80ba-2036c482890c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436045.1_ASM143604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:25,457] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:25,460] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:25,461] [INFO] Target genome list was writen to GCF_001436045.1_ASM143604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:25,488] [INFO] Task started: fastANI
[2024-01-24 14:15:25,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe32fb82-9346-4631-81b0-3a7da3e524a6/GCF_001436045.1_ASM143604v1_genomic.fna.gz --refList GCF_001436045.1_ASM143604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436045.1_ASM143604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:31,957] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:31,972] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:31,973] [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_001436045.1	s__Limosilactobacillus frumenti	100.0	565	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.86	99.72	0.98	0.96	3	conclusive
GCF_000159435.1	s__Limosilactobacillus vaginalis	80.0855	209	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.80	96.39	0.94	0.86	8	-
GCF_014836425.1	s__Limosilactobacillus sp014836425	79.897	208	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838735.1	s__Limosilactobacillus portuensis	79.7816	187	567	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	79.7747	188	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_014145505.1	s__Limosilactobacillus fastidiosus	79.7397	182	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	-
GCF_009663775.1	s__Limosilactobacillus sp009663775	79.2859	125	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	-
GCA_018883805.1	s__Limosilactobacillus merdavium	79.158	168	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.07	96.07	0.81	0.81	2	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	79.1233	157	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_000016825.1	s__Limosilactobacillus reuteri	79.0075	158	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.5043	82	567	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:31,974] [INFO] GTDB search result was written to GCF_001436045.1_ASM143604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:31,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:31,979] [INFO] DFAST_QC result json was written to GCF_001436045.1_ASM143604v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:31,979] [INFO] DFAST_QC completed!
[2024-01-24 14:15:31,979] [INFO] Total running time: 0h0m45s