[2023-06-13 16:36:02,054] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:36:02,057] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:36:02,057] [INFO] DQC Reference Directory: /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference
[2023-06-13 16:36:03,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:36:03,309] [INFO] Task started: Prodigal
[2023-06-13 16:36:03,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg1390bf89-e5c8-4c8e-b1ba-b5416904e4a8/GCA_022746725.1_ASM2274672v1_genomic.fna.gz | prodigal -d GCA_022746725.1_ASM2274672v1_genomic.fna/cds.fna -a GCA_022746725.1_ASM2274672v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:36:08,848] [INFO] Task succeeded: Prodigal
[2023-06-13 16:36:08,848] [INFO] Task started: HMMsearch
[2023-06-13 16:36:08,848] [INFO] Running command: hmmsearch --tblout GCA_022746725.1_ASM2274672v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/reference_markers.hmm GCA_022746725.1_ASM2274672v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:36:09,028] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:36:09,029] [INFO] Found 6/6 markers.
[2023-06-13 16:36:09,052] [INFO] Query marker FASTA was written to GCA_022746725.1_ASM2274672v1_genomic.fna/markers.fasta
[2023-06-13 16:36:09,053] [INFO] Task started: Blastn
[2023-06-13 16:36:09,053] [INFO] Running command: blastn -query GCA_022746725.1_ASM2274672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/reference_markers.fasta -out GCA_022746725.1_ASM2274672v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:09,618] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:09,624] [INFO] Selected 14 target genomes.
[2023-06-13 16:36:09,625] [INFO] Target genome list was writen to GCA_022746725.1_ASM2274672v1_genomic.fna/target_genomes.txt
[2023-06-13 16:36:09,626] [INFO] Task started: fastANI
[2023-06-13 16:36:09,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg1390bf89-e5c8-4c8e-b1ba-b5416904e4a8/GCA_022746725.1_ASM2274672v1_genomic.fna.gz --refList GCA_022746725.1_ASM2274672v1_genomic.fna/target_genomes.txt --output GCA_022746725.1_ASM2274672v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:36:15,649] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:15,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:36:15,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:36:15,657] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 16:36:15,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 16:36:15,657] [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
Ligilactobacillus ruminis	strain=NBRC 102161	GCA_001591905.1	1623	1623	type	True	96.539	528	698	95	conclusive
Ligilactobacillus ruminis	strain=DSM 20403	GCA_001436475.1	1623	1623	type	True	96.5193	539	698	95	conclusive
Ligilactobacillus ruminis	strain=DSM 20403	GCA_900113455.1	1623	1623	type	True	96.5145	556	698	95	conclusive
Ligilactobacillus ruminis	strain=ATCC 27780	GCA_001008755.1	1623	1623	type	True	96.5	545	698	95	conclusive
Ligilactobacillus murinus	strain=DSM 20452	GCA_001436015.1	1622	1622	type	True	79.62	51	698	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	79.4709	53	698	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:36:15,659] [INFO] DFAST Taxonomy check result was written to GCA_022746725.1_ASM2274672v1_genomic.fna/tc_result.tsv
[2023-06-13 16:36:15,660] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:36:15,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:36:15,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/checkm_data
[2023-06-13 16:36:15,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:36:15,687] [INFO] Task started: CheckM
[2023-06-13 16:36:15,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022746725.1_ASM2274672v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022746725.1_ASM2274672v1_genomic.fna/checkm_input GCA_022746725.1_ASM2274672v1_genomic.fna/checkm_result
[2023-06-13 16:36:38,636] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:38,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:38,656] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:38,656] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:38,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022746725.1_ASM2274672v1_genomic.fna/markers.fasta)
[2023-06-13 16:36:38,657] [INFO] Task started: Blastn
[2023-06-13 16:36:38,657] [INFO] Running command: blastn -query GCA_022746725.1_ASM2274672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd45c5a87-9fe4-4f64-9f31-3333a157f16c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022746725.1_ASM2274672v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:39,383] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:39,388] [INFO] Selected 27 target genomes.
[2023-06-13 16:36:39,388] [INFO] Target genome list was writen to GCA_022746725.1_ASM2274672v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:39,392] [INFO] Task started: fastANI
[2023-06-13 16:36:39,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg1390bf89-e5c8-4c8e-b1ba-b5416904e4a8/GCA_022746725.1_ASM2274672v1_genomic.fna.gz --refList GCA_022746725.1_ASM2274672v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022746725.1_ASM2274672v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:49,289] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:49,294] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:36:49,294] [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_900113455.1	s__Ligilactobacillus ruminis	96.5145	556	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.28	96.58	0.88	0.79	57	conclusive
GCF_900110005.1	s__Ligilactobacillus ruminis_A	79.9259	141	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCF_001434535.1	s__Ligilactobacillus animalis	79.7691	51	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	78.959	55	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:49,296] [INFO] GTDB search result was written to GCA_022746725.1_ASM2274672v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:49,297] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:49,299] [INFO] DFAST_QC result json was written to GCA_022746725.1_ASM2274672v1_genomic.fna/dqc_result.json
[2023-06-13 16:36:49,299] [INFO] DFAST_QC completed!
[2023-06-13 16:36:49,299] [INFO] Total running time: 0h0m47s