[2023-06-29 16:38:52,324] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:38:52,330] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:38:52,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference
[2023-06-29 16:38:53,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:38:53,679] [INFO] Task started: Prodigal
[2023-06-29 16:38:53,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg2afce77f-173f-4ef4-948b-a266f02c3869/GCA_910584565.1_MGBC123951_genomic.fna.gz | prodigal -d GCA_910584565.1_MGBC123951_genomic.fna/cds.fna -a GCA_910584565.1_MGBC123951_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:38:57,209] [INFO] Task succeeded: Prodigal
[2023-06-29 16:38:57,209] [INFO] Task started: HMMsearch
[2023-06-29 16:38:57,209] [INFO] Running command: hmmsearch --tblout GCA_910584565.1_MGBC123951_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/reference_markers.hmm GCA_910584565.1_MGBC123951_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:38:57,499] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:38:57,500] [INFO] Found 6/6 markers.
[2023-06-29 16:38:57,521] [INFO] Query marker FASTA was written to GCA_910584565.1_MGBC123951_genomic.fna/markers.fasta
[2023-06-29 16:38:57,521] [INFO] Task started: Blastn
[2023-06-29 16:38:57,522] [INFO] Running command: blastn -query GCA_910584565.1_MGBC123951_genomic.fna/markers.fasta -db /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/reference_markers.fasta -out GCA_910584565.1_MGBC123951_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:38:58,121] [INFO] Task succeeded: Blastn
[2023-06-29 16:38:58,125] [INFO] Selected 6 target genomes.
[2023-06-29 16:38:58,125] [INFO] Target genome list was writen to GCA_910584565.1_MGBC123951_genomic.fna/target_genomes.txt
[2023-06-29 16:38:58,126] [INFO] Task started: fastANI
[2023-06-29 16:38:58,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afce77f-173f-4ef4-948b-a266f02c3869/GCA_910584565.1_MGBC123951_genomic.fna.gz --refList GCA_910584565.1_MGBC123951_genomic.fna/target_genomes.txt --output GCA_910584565.1_MGBC123951_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:39:01,115] [INFO] Task succeeded: fastANI
[2023-06-29 16:39:01,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:39:01,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:39:01,122] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 16:39:01,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 16:39:01,123] [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 urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	97.5862	486	566	95	conclusive
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	92.8401	489	566	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	90.8732	428	566	95	below_threshold
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	90.6358	485	566	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	83.4874	361	566	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:39:01,124] [INFO] DFAST Taxonomy check result was written to GCA_910584565.1_MGBC123951_genomic.fna/tc_result.tsv
[2023-06-29 16:39:01,125] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:39:01,125] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:39:01,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/checkm_data
[2023-06-29 16:39:01,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:39:01,151] [INFO] Task started: CheckM
[2023-06-29 16:39:01,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910584565.1_MGBC123951_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910584565.1_MGBC123951_genomic.fna/checkm_input GCA_910584565.1_MGBC123951_genomic.fna/checkm_result
[2023-06-29 16:39:19,781] [INFO] Task succeeded: CheckM
[2023-06-29 16:39:19,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:39:19,800] [INFO] ===== Completeness check finished =====
[2023-06-29 16:39:19,801] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:39:19,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910584565.1_MGBC123951_genomic.fna/markers.fasta)
[2023-06-29 16:39:19,802] [INFO] Task started: Blastn
[2023-06-29 16:39:19,802] [INFO] Running command: blastn -query GCA_910584565.1_MGBC123951_genomic.fna/markers.fasta -db /var/lib/cwl/stg56dc362d-a809-4390-9492-247788625284/dqc_reference/reference_markers_gtdb.fasta -out GCA_910584565.1_MGBC123951_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:39:20,629] [INFO] Task succeeded: Blastn
[2023-06-29 16:39:20,633] [INFO] Selected 7 target genomes.
[2023-06-29 16:39:20,634] [INFO] Target genome list was writen to GCA_910584565.1_MGBC123951_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:39:20,640] [INFO] Task started: fastANI
[2023-06-29 16:39:20,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg2afce77f-173f-4ef4-948b-a266f02c3869/GCA_910584565.1_MGBC123951_genomic.fna.gz --refList GCA_910584565.1_MGBC123951_genomic.fna/target_genomes_gtdb.txt --output GCA_910584565.1_MGBC123951_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:39:23,985] [INFO] Task succeeded: fastANI
[2023-06-29 16:39:23,992] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:39:23,993] [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_014838745.1	s__Limosilactobacillus urinaemulieris	97.5862	486	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	conclusive
GCF_014838735.1	s__Limosilactobacillus portuensis	92.828	490	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.50	97.46	0.87	0.84	6	-
GCF_000159435.1	s__Limosilactobacillus vaginalis	90.6358	485	566	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	83.5102	360	566	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	82.425	322	566	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	81.416	275	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.07	96.07	0.81	0.81	2	-
GCF_009663775.1	s__Limosilactobacillus sp009663775	80.3922	165	566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-29 16:39:23,995] [INFO] GTDB search result was written to GCA_910584565.1_MGBC123951_genomic.fna/result_gtdb.tsv
[2023-06-29 16:39:23,995] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:39:23,998] [INFO] DFAST_QC result json was written to GCA_910584565.1_MGBC123951_genomic.fna/dqc_result.json
[2023-06-29 16:39:23,999] [INFO] DFAST_QC completed!
[2023-06-29 16:39:23,999] [INFO] Total running time: 0h0m32s