[2023-06-13 06:11:18,497] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:18,499] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:18,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference
[2023-06-13 06:11:20,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:20,217] [INFO] Task started: Prodigal
[2023-06-13 06:11:20,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgef3fd695-74d3-4b1b-b9e2-6fd83b580b3b/GCA_022753365.1_ASM2275336v1_genomic.fna.gz | prodigal -d GCA_022753365.1_ASM2275336v1_genomic.fna/cds.fna -a GCA_022753365.1_ASM2275336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:20,847] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:20,848] [INFO] Task started: HMMsearch
[2023-06-13 06:11:20,848] [INFO] Running command: hmmsearch --tblout GCA_022753365.1_ASM2275336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/reference_markers.hmm GCA_022753365.1_ASM2275336v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:21,058] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:21,060] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgef3fd695-74d3-4b1b-b9e2-6fd83b580b3b/GCA_022753365.1_ASM2275336v1_genomic.fna.gz]
[2023-06-13 06:11:21,097] [INFO] Query marker FASTA was written to GCA_022753365.1_ASM2275336v1_genomic.fna/markers.fasta
[2023-06-13 06:11:21,097] [INFO] Task started: Blastn
[2023-06-13 06:11:21,097] [INFO] Running command: blastn -query GCA_022753365.1_ASM2275336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/reference_markers.fasta -out GCA_022753365.1_ASM2275336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:21,733] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:21,737] [INFO] Selected 11 target genomes.
[2023-06-13 06:11:21,737] [INFO] Target genome list was writen to GCA_022753365.1_ASM2275336v1_genomic.fna/target_genomes.txt
[2023-06-13 06:11:21,780] [INFO] Task started: fastANI
[2023-06-13 06:11:21,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3fd695-74d3-4b1b-b9e2-6fd83b580b3b/GCA_022753365.1_ASM2275336v1_genomic.fna.gz --refList GCA_022753365.1_ASM2275336v1_genomic.fna/target_genomes.txt --output GCA_022753365.1_ASM2275336v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:25,751] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:25,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:25,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:25,760] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 06:11:25,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 06:11:25,760] [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
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.8467	89	98	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.6401	94	98	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 06:11:25,762] [INFO] DFAST Taxonomy check result was written to GCA_022753365.1_ASM2275336v1_genomic.fna/tc_result.tsv
[2023-06-13 06:11:25,763] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:25,763] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:25,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/checkm_data
[2023-06-13 06:11:25,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:25,776] [INFO] Task started: CheckM
[2023-06-13 06:11:25,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022753365.1_ASM2275336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022753365.1_ASM2275336v1_genomic.fna/checkm_input GCA_022753365.1_ASM2275336v1_genomic.fna/checkm_result
[2023-06-13 06:11:37,787] [INFO] Task succeeded: CheckM
[2023-06-13 06:11:37,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:11:37,805] [INFO] ===== Completeness check finished =====
[2023-06-13 06:11:37,805] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:11:37,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022753365.1_ASM2275336v1_genomic.fna/markers.fasta)
[2023-06-13 06:11:37,806] [INFO] Task started: Blastn
[2023-06-13 06:11:37,806] [INFO] Running command: blastn -query GCA_022753365.1_ASM2275336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841e4f48-ab5d-4e28-8b32-4690639b5428/dqc_reference/reference_markers_gtdb.fasta -out GCA_022753365.1_ASM2275336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:38,328] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:38,335] [INFO] Selected 13 target genomes.
[2023-06-13 06:11:38,335] [INFO] Target genome list was writen to GCA_022753365.1_ASM2275336v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:11:38,358] [INFO] Task started: fastANI
[2023-06-13 06:11:38,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3fd695-74d3-4b1b-b9e2-6fd83b580b3b/GCA_022753365.1_ASM2275336v1_genomic.fna.gz --refList GCA_022753365.1_ASM2275336v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022753365.1_ASM2275336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:11:42,151] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:42,154] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:11:42,154] [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_000160875.1	s__Lactobacillus iners	98.8467	89	98	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
--------------------------------------------------------------------------------
[2023-06-13 06:11:42,156] [INFO] GTDB search result was written to GCA_022753365.1_ASM2275336v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:11:42,157] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:11:42,159] [INFO] DFAST_QC result json was written to GCA_022753365.1_ASM2275336v1_genomic.fna/dqc_result.json
[2023-06-13 06:11:42,159] [INFO] DFAST_QC completed!
[2023-06-13 06:11:42,160] [INFO] Total running time: 0h0m24s