[2024-01-24 14:21:50,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference
[2024-01-24 14:21:52,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,204] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca87d39-fca9-4417-978b-e6c86b57e4ef/GCF_014145505.1_ASM1414550v1_genomic.fna.gz | prodigal -d GCF_014145505.1_ASM1414550v1_genomic.fna/cds.fna -a GCF_014145505.1_ASM1414550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:21:55,815] [INFO] Task succeeded: Prodigal
[2024-01-24 14:21:55,815] [INFO] Task started: HMMsearch
[2024-01-24 14:21:55,815] [INFO] Running command: hmmsearch --tblout GCF_014145505.1_ASM1414550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/reference_markers.hmm GCF_014145505.1_ASM1414550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:21:56,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:21:56,074] [INFO] Found 6/6 markers.
[2024-01-24 14:21:56,094] [INFO] Query marker FASTA was written to GCF_014145505.1_ASM1414550v1_genomic.fna/markers.fasta
[2024-01-24 14:21:56,095] [INFO] Task started: Blastn
[2024-01-24 14:21:56,095] [INFO] Running command: blastn -query GCF_014145505.1_ASM1414550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/reference_markers.fasta -out GCF_014145505.1_ASM1414550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:56,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:56,731] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:56,731] [INFO] Target genome list was writen to GCF_014145505.1_ASM1414550v1_genomic.fna/target_genomes.txt
[2024-01-24 14:21:56,743] [INFO] Task started: fastANI
[2024-01-24 14:21:56,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca87d39-fca9-4417-978b-e6c86b57e4ef/GCF_014145505.1_ASM1414550v1_genomic.fna.gz --refList GCF_014145505.1_ASM1414550v1_genomic.fna/target_genomes.txt --output GCF_014145505.1_ASM1414550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:00,657] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:00,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:00,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:00,666] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:00,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:00,666] [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 fastidiosus	strain=WF-MO7-1	GCA_014145505.1	2759855	2759855	type	True	100.0	554	557	95	conclusive
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	90.4832	431	557	95	below_threshold
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	82.9075	381	557	95	below_threshold
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	82.6461	360	557	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	82.5156	335	557	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	82.3505	365	557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:00,668] [INFO] DFAST Taxonomy check result was written to GCF_014145505.1_ASM1414550v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:00,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:00,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:00,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/checkm_data
[2024-01-24 14:22:00,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:00,691] [INFO] Task started: CheckM
[2024-01-24 14:22:00,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145505.1_ASM1414550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145505.1_ASM1414550v1_genomic.fna/checkm_input GCF_014145505.1_ASM1414550v1_genomic.fna/checkm_result
[2024-01-24 14:22:19,022] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:19,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:19,044] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:19,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:19,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145505.1_ASM1414550v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:19,046] [INFO] Task started: Blastn
[2024-01-24 14:22:19,046] [INFO] Running command: blastn -query GCF_014145505.1_ASM1414550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a5705de-715c-4ff7-900c-aab2cad5c43f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145505.1_ASM1414550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:19,882] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:19,885] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:19,886] [INFO] Target genome list was writen to GCF_014145505.1_ASM1414550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:19,903] [INFO] Task started: fastANI
[2024-01-24 14:22:19,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca87d39-fca9-4417-978b-e6c86b57e4ef/GCF_014145505.1_ASM1414550v1_genomic.fna.gz --refList GCF_014145505.1_ASM1414550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145505.1_ASM1414550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:23,898] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:23,927] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:23,927] [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_014145505.1	s__Limosilactobacillus fastidiosus	100.0	554	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	conclusive
GCF_014836425.1	s__Limosilactobacillus sp014836425	90.4619	432	557	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	82.8901	381	557	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	82.657	359	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.80	96.39	0.94	0.86	8	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	82.372	364	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCA_018883805.1	s__Limosilactobacillus merdavium	81.2837	244	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.07	96.07	0.81	0.81	2	-
GCF_000016825.1	s__Limosilactobacillus reuteri	79.5087	163	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	79.4675	160	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_014145585.1	s__Limosilactobacillus agrestis	79.1143	160	557	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:23,930] [INFO] GTDB search result was written to GCF_014145505.1_ASM1414550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:23,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:23,935] [INFO] DFAST_QC result json was written to GCF_014145505.1_ASM1414550v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:23,935] [INFO] DFAST_QC completed!
[2024-01-24 14:22:23,935] [INFO] Total running time: 0h0m33s