[2024-01-25 19:58:50,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:50,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:50,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference
[2024-01-25 19:58:51,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:51,912] [INFO] Task started: Prodigal
[2024-01-25 19:58:51,912] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ebe5617-5099-40de-baa4-65b554ddb21f/GCF_001438685.1_ASM143868v1_genomic.fna.gz | prodigal -d GCF_001438685.1_ASM143868v1_genomic.fna/cds.fna -a GCF_001438685.1_ASM143868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:54,363] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:54,364] [INFO] Task started: HMMsearch
[2024-01-25 19:58:54,364] [INFO] Running command: hmmsearch --tblout GCF_001438685.1_ASM143868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/reference_markers.hmm GCF_001438685.1_ASM143868v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:54,578] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:54,583] [INFO] Found 6/6 markers.
[2024-01-25 19:58:54,601] [INFO] Query marker FASTA was written to GCF_001438685.1_ASM143868v1_genomic.fna/markers.fasta
[2024-01-25 19:58:54,601] [INFO] Task started: Blastn
[2024-01-25 19:58:54,601] [INFO] Running command: blastn -query GCF_001438685.1_ASM143868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/reference_markers.fasta -out GCF_001438685.1_ASM143868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:55,161] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:55,164] [INFO] Selected 13 target genomes.
[2024-01-25 19:58:55,164] [INFO] Target genome list was writen to GCF_001438685.1_ASM143868v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:55,176] [INFO] Task started: fastANI
[2024-01-25 19:58:55,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ebe5617-5099-40de-baa4-65b554ddb21f/GCF_001438685.1_ASM143868v1_genomic.fna.gz --refList GCF_001438685.1_ASM143868v1_genomic.fna/target_genomes.txt --output GCF_001438685.1_ASM143868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:59,702] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:59,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:59,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:59,708] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:58:59,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:59,709] [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
Fructilactobacillus lindneri	strain=DSM 20690	GCA_001438685.1	53444	53444	type	True	100.0	467	467	95	conclusive
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	99.9918	464	467	95	conclusive
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	99.9464	458	467	95	conclusive
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	79.5456	189	467	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	79.361	202	467	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	78.1785	57	467	95	below_threshold
Apilactobacillus xinyiensis	strain=F575-4	GCA_019656235.1	2841032	2841032	type	True	77.643	66	467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:59,711] [INFO] DFAST Taxonomy check result was written to GCF_001438685.1_ASM143868v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:59,712] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:59,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:59,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/checkm_data
[2024-01-25 19:58:59,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:59,738] [INFO] Task started: CheckM
[2024-01-25 19:58:59,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001438685.1_ASM143868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001438685.1_ASM143868v1_genomic.fna/checkm_input GCF_001438685.1_ASM143868v1_genomic.fna/checkm_result
[2024-01-25 19:59:13,735] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:13,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:13,751] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:13,751] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:13,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001438685.1_ASM143868v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:13,752] [INFO] Task started: Blastn
[2024-01-25 19:59:13,752] [INFO] Running command: blastn -query GCF_001438685.1_ASM143868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36897fec-a1d3-413f-8c99-2f34d4204d44/dqc_reference/reference_markers_gtdb.fasta -out GCF_001438685.1_ASM143868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:14,462] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:14,464] [INFO] Selected 22 target genomes.
[2024-01-25 19:59:14,465] [INFO] Target genome list was writen to GCF_001438685.1_ASM143868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:14,495] [INFO] Task started: fastANI
[2024-01-25 19:59:14,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ebe5617-5099-40de-baa4-65b554ddb21f/GCF_001438685.1_ASM143868v1_genomic.fna.gz --refList GCF_001438685.1_ASM143868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001438685.1_ASM143868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:20,734] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:20,740] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:20,740] [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_002907375.1	s__Fructilactobacillus lindneri	99.9918	464	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	conclusive
GCF_001436035.1	s__Fructilactobacillus sanfranciscensis	79.2506	187	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	-
GCF_002993975.1	s__Apilactobacillus micheneri	78.1785	57	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
GCF_002993965.1	s__Apilactobacillus timberlakei	78.0769	56	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.96	98.30	0.93	0.87	9	-
GCF_002994005.1	s__Apilactobacillus quenuiae	77.8131	59	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436645.1	s__Fructilactobacillus florum	77.7052	71	467	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.34	99.05	0.97	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:20,747] [INFO] GTDB search result was written to GCF_001438685.1_ASM143868v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:20,748] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:20,751] [INFO] DFAST_QC result json was written to GCF_001438685.1_ASM143868v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:20,751] [INFO] DFAST_QC completed!
[2024-01-25 19:59:20,751] [INFO] Total running time: 0h0m30s