[2024-01-24 14:37:46,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference
[2024-01-24 14:37:50,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,274] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg15feae23-c5a3-4cc4-8cd7-85d03bea1c43/GCF_003369815.1_ASM336981v1_genomic.fna.gz | prodigal -d GCF_003369815.1_ASM336981v1_genomic.fna/cds.fna -a GCF_003369815.1_ASM336981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:37:52,896] [INFO] Task succeeded: Prodigal
[2024-01-24 14:37:52,897] [INFO] Task started: HMMsearch
[2024-01-24 14:37:52,897] [INFO] Running command: hmmsearch --tblout GCF_003369815.1_ASM336981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/reference_markers.hmm GCF_003369815.1_ASM336981v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:37:53,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:37:53,237] [INFO] Found 6/6 markers.
[2024-01-24 14:37:53,254] [INFO] Query marker FASTA was written to GCF_003369815.1_ASM336981v1_genomic.fna/markers.fasta
[2024-01-24 14:37:53,254] [INFO] Task started: Blastn
[2024-01-24 14:37:53,254] [INFO] Running command: blastn -query GCF_003369815.1_ASM336981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/reference_markers.fasta -out GCF_003369815.1_ASM336981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:37:57,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:37:57,318] [INFO] Selected 14 target genomes.
[2024-01-24 14:37:57,318] [INFO] Target genome list was writen to GCF_003369815.1_ASM336981v1_genomic.fna/target_genomes.txt
[2024-01-24 14:37:57,353] [INFO] Task started: fastANI
[2024-01-24 14:37:57,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg15feae23-c5a3-4cc4-8cd7-85d03bea1c43/GCF_003369815.1_ASM336981v1_genomic.fna.gz --refList GCF_003369815.1_ASM336981v1_genomic.fna/target_genomes.txt --output GCF_003369815.1_ASM336981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:01,507] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:01,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:01,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:01,525] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:38:01,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:01,526] [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 sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	100.0	400	401	95	conclusive
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	99.989	399	401	95	conclusive
Fructilactobacillus sanfranciscensis	strain=DSM 20451	GCA_001436035.1	1625	1625	type	True	99.8658	365	401	95	conclusive
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	79.5025	194	401	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	79.2886	196	401	95	below_threshold
Apilactobacillus ozensis	strain=JCM 17196	GCA_001311485.1	866801	866801	type	True	78.38	55	401	95	below_threshold
Apilactobacillus micheneri	strain=Hlig3	GCA_002993975.1	1899430	1899430	type	True	78.1932	65	401	95	below_threshold
Fructilactobacillus florum	strain=JCM 16035	GCA_001311215.1	640331	640331	type	True	77.7337	64	401	95	below_threshold
Apilactobacillus quenuiae	strain=HV_6	GCA_002994005.1	2008377	2008377	type	True	77.5675	66	401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:01,528] [INFO] DFAST Taxonomy check result was written to GCF_003369815.1_ASM336981v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:01,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:01,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:01,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/checkm_data
[2024-01-24 14:38:01,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:01,549] [INFO] Task started: CheckM
[2024-01-24 14:38:01,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003369815.1_ASM336981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003369815.1_ASM336981v1_genomic.fna/checkm_input GCF_003369815.1_ASM336981v1_genomic.fna/checkm_result
[2024-01-24 14:38:23,174] [INFO] Task succeeded: CheckM
[2024-01-24 14:38:23,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:38:23,196] [INFO] ===== Completeness check finished =====
[2024-01-24 14:38:23,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:38:23,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003369815.1_ASM336981v1_genomic.fna/markers.fasta)
[2024-01-24 14:38:23,197] [INFO] Task started: Blastn
[2024-01-24 14:38:23,197] [INFO] Running command: blastn -query GCF_003369815.1_ASM336981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050e11b2-dbd7-44b6-be03-bd595d5af4ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_003369815.1_ASM336981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:23,976] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:23,981] [INFO] Selected 21 target genomes.
[2024-01-24 14:38:23,981] [INFO] Target genome list was writen to GCF_003369815.1_ASM336981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:38:23,999] [INFO] Task started: fastANI
[2024-01-24 14:38:23,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg15feae23-c5a3-4cc4-8cd7-85d03bea1c43/GCF_003369815.1_ASM336981v1_genomic.fna.gz --refList GCF_003369815.1_ASM336981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003369815.1_ASM336981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:38:30,912] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:30,922] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:38:30,922] [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_001436035.1	s__Fructilactobacillus sanfranciscensis	99.8658	365	401	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	conclusive
GCF_002907375.1	s__Fructilactobacillus lindneri	79.5025	194	401	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	-
GCF_002993975.1	s__Apilactobacillus micheneri	78.1932	65	401	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	77.9277	66	401	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	77.5675	66	401	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:38:30,931] [INFO] GTDB search result was written to GCF_003369815.1_ASM336981v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:38:30,932] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:38:30,937] [INFO] DFAST_QC result json was written to GCF_003369815.1_ASM336981v1_genomic.fna/dqc_result.json
[2024-01-24 14:38:30,937] [INFO] DFAST_QC completed!
[2024-01-24 14:38:30,937] [INFO] Total running time: 0h0m44s