[2024-01-24 13:17:04,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference
[2024-01-24 13:17:05,398] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:05,401] [INFO] Task started: Prodigal
[2024-01-24 13:17:05,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bebc91f-e268-47bb-9ccd-eb971e73ea78/GCF_000284335.1_ASM28433v1_genomic.fna.gz | prodigal -d GCF_000284335.1_ASM28433v1_genomic.fna/cds.fna -a GCF_000284335.1_ASM28433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:08,867] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:08,868] [INFO] Task started: HMMsearch
[2024-01-24 13:17:08,868] [INFO] Running command: hmmsearch --tblout GCF_000284335.1_ASM28433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/reference_markers.hmm GCF_000284335.1_ASM28433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:09,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:09,092] [INFO] Found 6/6 markers.
[2024-01-24 13:17:09,110] [INFO] Query marker FASTA was written to GCF_000284335.1_ASM28433v1_genomic.fna/markers.fasta
[2024-01-24 13:17:09,110] [INFO] Task started: Blastn
[2024-01-24 13:17:09,111] [INFO] Running command: blastn -query GCF_000284335.1_ASM28433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/reference_markers.fasta -out GCF_000284335.1_ASM28433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:09,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:09,675] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:09,676] [INFO] Target genome list was writen to GCF_000284335.1_ASM28433v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:09,681] [INFO] Task started: fastANI
[2024-01-24 13:17:09,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bebc91f-e268-47bb-9ccd-eb971e73ea78/GCF_000284335.1_ASM28433v1_genomic.fna.gz --refList GCF_000284335.1_ASM28433v1_genomic.fna/target_genomes.txt --output GCF_000284335.1_ASM28433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:17,719] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:17,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:17,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:17,723] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:17,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:17,724] [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
Caldisericum exile	strain=AZM16c01	GCA_000284335.1	693075	693075	type	True	100.0	519	519	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:17,725] [INFO] DFAST Taxonomy check result was written to GCF_000284335.1_ASM28433v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:17,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:17,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:17,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/checkm_data
[2024-01-24 13:17:17,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:17,748] [INFO] Task started: CheckM
[2024-01-24 13:17:17,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000284335.1_ASM28433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000284335.1_ASM28433v1_genomic.fna/checkm_input GCF_000284335.1_ASM28433v1_genomic.fna/checkm_result
[2024-01-24 13:17:36,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:36,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:36,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:36,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:36,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000284335.1_ASM28433v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:36,239] [INFO] Task started: Blastn
[2024-01-24 13:17:36,239] [INFO] Running command: blastn -query GCF_000284335.1_ASM28433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c4d1846-9a01-449a-8831-facbf5865611/dqc_reference/reference_markers_gtdb.fasta -out GCF_000284335.1_ASM28433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:37,104] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:37,107] [INFO] Selected 18 target genomes.
[2024-01-24 13:17:37,107] [INFO] Target genome list was writen to GCF_000284335.1_ASM28433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:37,172] [INFO] Task started: fastANI
[2024-01-24 13:17:37,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bebc91f-e268-47bb-9ccd-eb971e73ea78/GCF_000284335.1_ASM28433v1_genomic.fna.gz --refList GCF_000284335.1_ASM28433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000284335.1_ASM28433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:44,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:44,734] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:44,735] [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_000284335.1	s__Caldisericum exile	100.0	519	519	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Caldisericales;f__Caldisericaceae;g__Caldisericum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002877955.1	s__Caldisericum exile_A	80.0585	183	519	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Caldisericales;f__Caldisericaceae;g__Caldisericum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334675.1	s__Caldisericum exile_B	78.0719	63	519	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Caldisericales;f__Caldisericaceae;g__Caldisericum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:44,736] [INFO] GTDB search result was written to GCF_000284335.1_ASM28433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:44,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:44,739] [INFO] DFAST_QC result json was written to GCF_000284335.1_ASM28433v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:44,739] [INFO] DFAST_QC completed!
[2024-01-24 13:17:44,739] [INFO] Total running time: 0h0m41s