[2024-01-25 17:40:05,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference
[2024-01-25 17:40:06,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,665] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg543a6d0c-1a1f-49db-9a70-a6bb821476ca/GCF_014838735.1_ASM1483873v1_genomic.fna.gz | prodigal -d GCF_014838735.1_ASM1483873v1_genomic.fna/cds.fna -a GCF_014838735.1_ASM1483873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:10,248] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:10,249] [INFO] Task started: HMMsearch
[2024-01-25 17:40:10,249] [INFO] Running command: hmmsearch --tblout GCF_014838735.1_ASM1483873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/reference_markers.hmm GCF_014838735.1_ASM1483873v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:10,437] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:10,438] [INFO] Found 6/6 markers.
[2024-01-25 17:40:10,456] [INFO] Query marker FASTA was written to GCF_014838735.1_ASM1483873v1_genomic.fna/markers.fasta
[2024-01-25 17:40:10,457] [INFO] Task started: Blastn
[2024-01-25 17:40:10,457] [INFO] Running command: blastn -query GCF_014838735.1_ASM1483873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/reference_markers.fasta -out GCF_014838735.1_ASM1483873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:11,009] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:11,011] [INFO] Selected 10 target genomes.
[2024-01-25 17:40:11,012] [INFO] Target genome list was writen to GCF_014838735.1_ASM1483873v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:11,019] [INFO] Task started: fastANI
[2024-01-25 17:40:11,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg543a6d0c-1a1f-49db-9a70-a6bb821476ca/GCF_014838735.1_ASM1483873v1_genomic.fna.gz --refList GCF_014838735.1_ASM1483873v1_genomic.fna/target_genomes.txt --output GCF_014838735.1_ASM1483873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:15,640] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:15,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:15,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:15,646] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:15,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:15,646] [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 portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	100.0	658	660	95	conclusive
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	93.0487	531	660	95	below_threshold
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	91.5352	510	660	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	91.4883	463	660	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	83.7324	395	660	95	below_threshold
Limosilactobacillus fastidiosus	strain=WF-MO7-1	GCA_014145505.1	2759855	2759855	type	True	82.9609	376	660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:15,647] [INFO] DFAST Taxonomy check result was written to GCF_014838735.1_ASM1483873v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:15,648] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:15,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:15,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/checkm_data
[2024-01-25 17:40:15,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:15,673] [INFO] Task started: CheckM
[2024-01-25 17:40:15,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014838735.1_ASM1483873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014838735.1_ASM1483873v1_genomic.fna/checkm_input GCF_014838735.1_ASM1483873v1_genomic.fna/checkm_result
[2024-01-25 17:40:32,554] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:32,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:32,572] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:32,573] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:32,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014838735.1_ASM1483873v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:32,573] [INFO] Task started: Blastn
[2024-01-25 17:40:32,573] [INFO] Running command: blastn -query GCF_014838735.1_ASM1483873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddf66ac-34fe-4521-9b97-54bb57c45bb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014838735.1_ASM1483873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:33,330] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:33,332] [INFO] Selected 6 target genomes.
[2024-01-25 17:40:33,333] [INFO] Target genome list was writen to GCF_014838735.1_ASM1483873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:33,342] [INFO] Task started: fastANI
[2024-01-25 17:40:33,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg543a6d0c-1a1f-49db-9a70-a6bb821476ca/GCF_014838735.1_ASM1483873v1_genomic.fna.gz --refList GCF_014838735.1_ASM1483873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014838735.1_ASM1483873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:36,498] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:36,504] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:36,504] [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_014838735.1	s__Limosilactobacillus portuensis	100.0	658	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.50	97.46	0.87	0.84	6	conclusive
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	93.0683	530	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_000159435.1	s__Limosilactobacillus vaginalis	91.5352	510	660	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	83.7462	395	660	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	82.9492	375	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	-
GCF_900156885.1	s__Limosilactobacillus sp900156885	79.26	158	660	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:36,506] [INFO] GTDB search result was written to GCF_014838735.1_ASM1483873v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:36,506] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:36,509] [INFO] DFAST_QC result json was written to GCF_014838735.1_ASM1483873v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:36,509] [INFO] DFAST_QC completed!
[2024-01-25 17:40:36,509] [INFO] Total running time: 0h0m31s