[2024-01-24 10:47:08,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,932] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,933] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b8ade3b-56db-4fc8-863f-d5f01bc05150/GCF_001435585.1_ASM143558v1_genomic.fna.gz | prodigal -d GCF_001435585.1_ASM143558v1_genomic.fna/cds.fna -a GCF_001435585.1_ASM143558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,703] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,703] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,703] [INFO] Running command: hmmsearch --tblout GCF_001435585.1_ASM143558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/reference_markers.hmm GCF_001435585.1_ASM143558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,967] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,001] [INFO] Query marker FASTA was written to GCF_001435585.1_ASM143558v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,002] [INFO] Task started: Blastn
[2024-01-24 10:47:22,002] [INFO] Running command: blastn -query GCF_001435585.1_ASM143558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/reference_markers.fasta -out GCF_001435585.1_ASM143558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,661] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,664] [INFO] Selected 26 target genomes.
[2024-01-24 10:47:22,664] [INFO] Target genome list was writen to GCF_001435585.1_ASM143558v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,178] [INFO] Task started: fastANI
[2024-01-24 10:47:24,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b8ade3b-56db-4fc8-863f-d5f01bc05150/GCF_001435585.1_ASM143558v1_genomic.fna.gz --refList GCF_001435585.1_ASM143558v1_genomic.fna/target_genomes.txt --output GCF_001435585.1_ASM143558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:37,546] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:37,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:37,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:37,554] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:37,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:37,554] [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
Schleiferilactobacillus perolens	strain=DSM 12744	GCA_001435585.1	100468	100468	type	True	100.0	1070	1070	95	conclusive
Schleiferilactobacillus harbinensis	strain=DSM 16991	GCA_000425885.1	304207	304207	type	True	78.8781	294	1070	95	below_threshold
Schleiferilactobacillus harbinensis	strain=DSM 16991	GCA_001436325.1	304207	304207	type	True	78.8293	296	1070	95	below_threshold
Schleiferilactobacillus shenzhenensis	strain=LY-73	GCA_000469325.1	1231337	1231337	type	True	77.3491	186	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:37,557] [INFO] DFAST Taxonomy check result was written to GCF_001435585.1_ASM143558v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:37,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:37,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:37,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/checkm_data
[2024-01-24 10:47:37,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:37,594] [INFO] Task started: CheckM
[2024-01-24 10:47:37,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435585.1_ASM143558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435585.1_ASM143558v1_genomic.fna/checkm_input GCF_001435585.1_ASM143558v1_genomic.fna/checkm_result
[2024-01-24 10:48:11,249] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:11,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:11,274] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:11,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:11,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435585.1_ASM143558v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:11,275] [INFO] Task started: Blastn
[2024-01-24 10:48:11,275] [INFO] Running command: blastn -query GCF_001435585.1_ASM143558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f181cf-83fe-4cd4-83cb-109bf499abba/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435585.1_ASM143558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:12,099] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:12,104] [INFO] Selected 29 target genomes.
[2024-01-24 10:48:12,104] [INFO] Target genome list was writen to GCF_001435585.1_ASM143558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:12,150] [INFO] Task started: fastANI
[2024-01-24 10:48:12,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b8ade3b-56db-4fc8-863f-d5f01bc05150/GCF_001435585.1_ASM143558v1_genomic.fna.gz --refList GCF_001435585.1_ASM143558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435585.1_ASM143558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:26,413] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:26,418] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:26,418] [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_001435585.1	s__Schleiferilactobacillus perolens	100.0	1070	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425885.1	s__Schleiferilactobacillus harbinensis	78.853	295	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus	95.0	98.54	97.62	0.92	0.85	9	-
GCF_000469325.1	s__Schleiferilactobacillus shenzhenensis	77.3491	186	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,419] [INFO] GTDB search result was written to GCF_001435585.1_ASM143558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:26,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:26,423] [INFO] DFAST_QC result json was written to GCF_001435585.1_ASM143558v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:26,423] [INFO] DFAST_QC completed!
[2024-01-24 10:48:26,424] [INFO] Total running time: 0h1m18s