[2024-01-24 11:27:04,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference
[2024-01-24 11:27:05,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,740] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c5f1c92-e517-4804-a164-2d85aa747121/GCF_002998295.1_ASM299829v1_genomic.fna.gz | prodigal -d GCF_002998295.1_ASM299829v1_genomic.fna/cds.fna -a GCF_002998295.1_ASM299829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,987] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,988] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,988] [INFO] Running command: hmmsearch --tblout GCF_002998295.1_ASM299829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/reference_markers.hmm GCF_002998295.1_ASM299829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:09,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:09,228] [INFO] Found 6/6 markers.
[2024-01-24 11:27:09,245] [INFO] Query marker FASTA was written to GCF_002998295.1_ASM299829v1_genomic.fna/markers.fasta
[2024-01-24 11:27:09,246] [INFO] Task started: Blastn
[2024-01-24 11:27:09,246] [INFO] Running command: blastn -query GCF_002998295.1_ASM299829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/reference_markers.fasta -out GCF_002998295.1_ASM299829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,793] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,797] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:09,797] [INFO] Target genome list was writen to GCF_002998295.1_ASM299829v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,833] [INFO] Task started: fastANI
[2024-01-24 11:27:09,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5f1c92-e517-4804-a164-2d85aa747121/GCF_002998295.1_ASM299829v1_genomic.fna.gz --refList GCF_002998295.1_ASM299829v1_genomic.fna/target_genomes.txt --output GCF_002998295.1_ASM299829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:19,784] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:19,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:19,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:19,791] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:19,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:19,791] [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
Fastidiosipila sanguinis	strain=CCUG 47711	GCA_002998295.1	236753	236753	type	True	100.0	595	595	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:27:19,793] [INFO] DFAST Taxonomy check result was written to GCF_002998295.1_ASM299829v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:19,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:19,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:19,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/checkm_data
[2024-01-24 11:27:19,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:19,818] [INFO] Task started: CheckM
[2024-01-24 11:27:19,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002998295.1_ASM299829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002998295.1_ASM299829v1_genomic.fna/checkm_input GCF_002998295.1_ASM299829v1_genomic.fna/checkm_result
[2024-01-24 11:27:36,781] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:36,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,800] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:36,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:36,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002998295.1_ASM299829v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:36,801] [INFO] Task started: Blastn
[2024-01-24 11:27:36,802] [INFO] Running command: blastn -query GCF_002998295.1_ASM299829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb931632b-e791-4fdd-a40c-19f83e6d9a9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002998295.1_ASM299829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:37,546] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:37,551] [INFO] Selected 25 target genomes.
[2024-01-24 11:27:37,551] [INFO] Target genome list was writen to GCF_002998295.1_ASM299829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:37,574] [INFO] Task started: fastANI
[2024-01-24 11:27:37,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5f1c92-e517-4804-a164-2d85aa747121/GCF_002998295.1_ASM299829v1_genomic.fna.gz --refList GCF_002998295.1_ASM299829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002998295.1_ASM299829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:48,836] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:48,840] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:48,840] [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_002998295.1	s__Fastidiosipila sanguinis	100.0	595	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Fastidiosipilaceae;g__Fastidiosipila	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:27:48,841] [INFO] GTDB search result was written to GCF_002998295.1_ASM299829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:48,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:48,843] [INFO] DFAST_QC result json was written to GCF_002998295.1_ASM299829v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:48,843] [INFO] DFAST_QC completed!
[2024-01-24 11:27:48,844] [INFO] Total running time: 0h0m44s