[2024-01-24 11:34:55,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,369] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference
[2024-01-24 11:34:56,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,792] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg68a56afc-c362-4e45-b096-36407b273b3d/GCF_024029355.1_ASM2402935v1_genomic.fna.gz | prodigal -d GCF_024029355.1_ASM2402935v1_genomic.fna/cds.fna -a GCF_024029355.1_ASM2402935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:00,325] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:00,326] [INFO] Task started: HMMsearch
[2024-01-24 11:35:00,326] [INFO] Running command: hmmsearch --tblout GCF_024029355.1_ASM2402935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/reference_markers.hmm GCF_024029355.1_ASM2402935v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:00,567] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:00,568] [INFO] Found 6/6 markers.
[2024-01-24 11:35:00,594] [INFO] Query marker FASTA was written to GCF_024029355.1_ASM2402935v1_genomic.fna/markers.fasta
[2024-01-24 11:35:00,595] [INFO] Task started: Blastn
[2024-01-24 11:35:00,595] [INFO] Running command: blastn -query GCF_024029355.1_ASM2402935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/reference_markers.fasta -out GCF_024029355.1_ASM2402935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,603] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,608] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:01,609] [INFO] Target genome list was writen to GCF_024029355.1_ASM2402935v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,739] [INFO] Task started: fastANI
[2024-01-24 11:35:01,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a56afc-c362-4e45-b096-36407b273b3d/GCF_024029355.1_ASM2402935v1_genomic.fna.gz --refList GCF_024029355.1_ASM2402935v1_genomic.fna/target_genomes.txt --output GCF_024029355.1_ASM2402935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:07,935] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:07,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:07,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:07,958] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:07,958] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:07,959] [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 ixorae	strain=Ru20-1	GCA_024029915.1	1750535	1750535	type	True	80.6656	242	486	95	below_threshold
Fructilactobacillus lindneri	strain=TMW 1.88	GCA_002907375.1	53444	53444	type	True	78.4043	83	486	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_001438685.1	53444	53444	type	True	78.2254	82	486	95	below_threshold
Fructilactobacillus lindneri	strain=DSM 20690	GCA_900167245.1	53444	53444	type	True	78.1102	86	486	95	below_threshold
Fructilactobacillus florum	strain=JCM 16035	GCA_001311215.1	640331	640331	type	True	77.9459	59	486	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=TMW 1.53	GCA_002907365.1	1625	1625	type	True	77.9046	76	486	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=JCM 5668	GCA_003369815.1	1625	1625	type	True	77.7336	78	486	95	below_threshold
Fructilactobacillus sanfranciscensis	strain=DSM 20451	GCA_001436035.1	1625	1625	type	True	77.4204	75	486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:07,960] [INFO] DFAST Taxonomy check result was written to GCF_024029355.1_ASM2402935v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:07,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:07,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:07,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/checkm_data
[2024-01-24 11:35:07,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:07,985] [INFO] Task started: CheckM
[2024-01-24 11:35:07,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024029355.1_ASM2402935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024029355.1_ASM2402935v1_genomic.fna/checkm_input GCF_024029355.1_ASM2402935v1_genomic.fna/checkm_result
[2024-01-24 11:35:26,482] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:26,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:26,498] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:26,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:26,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024029355.1_ASM2402935v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:26,500] [INFO] Task started: Blastn
[2024-01-24 11:35:26,500] [INFO] Running command: blastn -query GCF_024029355.1_ASM2402935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89f2d65a-8aec-42f7-91e9-4354f02856dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_024029355.1_ASM2402935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:27,236] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:27,240] [INFO] Selected 29 target genomes.
[2024-01-24 11:35:27,240] [INFO] Target genome list was writen to GCF_024029355.1_ASM2402935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:27,262] [INFO] Task started: fastANI
[2024-01-24 11:35:27,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg68a56afc-c362-4e45-b096-36407b273b3d/GCF_024029355.1_ASM2402935v1_genomic.fna.gz --refList GCF_024029355.1_ASM2402935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024029355.1_ASM2402935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:37,333] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:37,342] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:35:37,343] [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	78.4043	83	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.90	99.78	0.98	0.96	12	-
GCF_001436645.1	s__Fructilactobacillus florum	77.7195	59	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.34	99.05	0.97	0.97	4	-
GCF_001436035.1	s__Fructilactobacillus sanfranciscensis	77.3805	76	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructilactobacillus	95.0	99.31	98.98	0.96	0.90	32	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,345] [INFO] GTDB search result was written to GCF_024029355.1_ASM2402935v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:37,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:37,350] [INFO] DFAST_QC result json was written to GCF_024029355.1_ASM2402935v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:37,350] [INFO] DFAST_QC completed!
[2024-01-24 11:35:37,351] [INFO] Total running time: 0h0m42s