[2024-01-24 15:10:54,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference
[2024-01-24 15:10:56,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,635] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgaabfdf4e-c11c-4d60-881c-1844a0ffb1fc/GCF_004339015.1_ASM433901v1_genomic.fna.gz | prodigal -d GCF_004339015.1_ASM433901v1_genomic.fna/cds.fna -a GCF_004339015.1_ASM433901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:06,904] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:06,904] [INFO] Task started: HMMsearch
[2024-01-24 15:11:06,904] [INFO] Running command: hmmsearch --tblout GCF_004339015.1_ASM433901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/reference_markers.hmm GCF_004339015.1_ASM433901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:07,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:07,246] [INFO] Found 6/6 markers.
[2024-01-24 15:11:07,292] [INFO] Query marker FASTA was written to GCF_004339015.1_ASM433901v1_genomic.fna/markers.fasta
[2024-01-24 15:11:07,292] [INFO] Task started: Blastn
[2024-01-24 15:11:07,292] [INFO] Running command: blastn -query GCF_004339015.1_ASM433901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/reference_markers.fasta -out GCF_004339015.1_ASM433901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:08,161] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:08,165] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:08,166] [INFO] Target genome list was writen to GCF_004339015.1_ASM433901v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:08,189] [INFO] Task started: fastANI
[2024-01-24 15:11:08,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgaabfdf4e-c11c-4d60-881c-1844a0ffb1fc/GCF_004339015.1_ASM433901v1_genomic.fna.gz --refList GCF_004339015.1_ASM433901v1_genomic.fna/target_genomes.txt --output GCF_004339015.1_ASM433901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:27,378] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:27,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:27,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:27,384] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:27,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:27,384] [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
Cocleimonas flava	strain=DSM 24830	GCA_004339015.1	634765	634765	type	True	100.0	1491	1491	95	conclusive
Leucothrix pacifica	strain=JCM 18388	GCA_003172875.1	1247513	1247513	type	True	76.9095	54	1491	95	below_threshold
Leucothrix mucor	strain=DSM 2157	GCA_000419525.1	45248	45248	type	True	76.3431	57	1491	95	below_threshold
Leucothrix arctica	strain=IMCC9719	GCA_003172895.1	1481894	1481894	type	True	76.1509	63	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:27,386] [INFO] DFAST Taxonomy check result was written to GCF_004339015.1_ASM433901v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:27,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:27,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:27,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/checkm_data
[2024-01-24 15:11:27,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:27,433] [INFO] Task started: CheckM
[2024-01-24 15:11:27,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339015.1_ASM433901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339015.1_ASM433901v1_genomic.fna/checkm_input GCF_004339015.1_ASM433901v1_genomic.fna/checkm_result
[2024-01-24 15:12:02,339] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:02,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:02,363] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:02,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:02,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339015.1_ASM433901v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:02,364] [INFO] Task started: Blastn
[2024-01-24 15:12:02,365] [INFO] Running command: blastn -query GCF_004339015.1_ASM433901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5215e8d0-6092-439c-8d87-158597ff2bfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339015.1_ASM433901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:03,458] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:03,462] [INFO] Selected 21 target genomes.
[2024-01-24 15:12:03,462] [INFO] Target genome list was writen to GCF_004339015.1_ASM433901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:03,478] [INFO] Task started: fastANI
[2024-01-24 15:12:03,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgaabfdf4e-c11c-4d60-881c-1844a0ffb1fc/GCF_004339015.1_ASM433901v1_genomic.fna.gz --refList GCF_004339015.1_ASM433901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339015.1_ASM433901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:15,877] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:15,882] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:15,883] [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_004339015.1	s__Cocleimonas flava	100.0	1491	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Cocleimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003172875.1	s__Leucothrix pacifica	76.9039	56	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Leucothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663245.1	s__Cocleimonas mucor_B	76.4301	56	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Cocleimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419525.1	s__Leucothrix mucor	76.3431	57	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Leucothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172895.1	s__Leucothrix arctica	76.1509	63	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Leucothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:15,884] [INFO] GTDB search result was written to GCF_004339015.1_ASM433901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:15,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:15,889] [INFO] DFAST_QC result json was written to GCF_004339015.1_ASM433901v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:15,890] [INFO] DFAST_QC completed!
[2024-01-24 15:12:15,890] [INFO] Total running time: 0h1m22s