[2024-01-25 18:54:35,459] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,460] [INFO] DQC Reference Directory: /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference
[2024-01-25 18:54:36,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,598] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg722d7d27-0611-4481-91d4-0c75f6ded389/GCF_030814315.1_ASM3081431v1_genomic.fna.gz | prodigal -d GCF_030814315.1_ASM3081431v1_genomic.fna/cds.fna -a GCF_030814315.1_ASM3081431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:42,834] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:42,834] [INFO] Task started: HMMsearch
[2024-01-25 18:54:42,834] [INFO] Running command: hmmsearch --tblout GCF_030814315.1_ASM3081431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/reference_markers.hmm GCF_030814315.1_ASM3081431v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:43,074] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:43,075] [INFO] Found 6/6 markers.
[2024-01-25 18:54:43,103] [INFO] Query marker FASTA was written to GCF_030814315.1_ASM3081431v1_genomic.fna/markers.fasta
[2024-01-25 18:54:43,104] [INFO] Task started: Blastn
[2024-01-25 18:54:43,104] [INFO] Running command: blastn -query GCF_030814315.1_ASM3081431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/reference_markers.fasta -out GCF_030814315.1_ASM3081431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:43,682] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:43,685] [INFO] Selected 17 target genomes.
[2024-01-25 18:54:43,685] [INFO] Target genome list was writen to GCF_030814315.1_ASM3081431v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:43,710] [INFO] Task started: fastANI
[2024-01-25 18:54:43,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg722d7d27-0611-4481-91d4-0c75f6ded389/GCF_030814315.1_ASM3081431v1_genomic.fna.gz --refList GCF_030814315.1_ASM3081431v1_genomic.fna/target_genomes.txt --output GCF_030814315.1_ASM3081431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:55,305] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:55,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:55,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:55,309] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:55,309] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:55,309] [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
Baia soyae	strain=DSM 46831	GCA_004341445.1	1544746	1544746	type	True	89.3996	824	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:55,311] [INFO] DFAST Taxonomy check result was written to GCF_030814315.1_ASM3081431v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:55,311] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:55,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:55,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/checkm_data
[2024-01-25 18:54:55,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:55,344] [INFO] Task started: CheckM
[2024-01-25 18:54:55,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814315.1_ASM3081431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814315.1_ASM3081431v1_genomic.fna/checkm_input GCF_030814315.1_ASM3081431v1_genomic.fna/checkm_result
[2024-01-25 18:55:18,543] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:18,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:18,567] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:18,568] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:18,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814315.1_ASM3081431v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:18,568] [INFO] Task started: Blastn
[2024-01-25 18:55:18,569] [INFO] Running command: blastn -query GCF_030814315.1_ASM3081431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90392f6-ed8d-47fa-962a-3808743eb090/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814315.1_ASM3081431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:19,539] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:19,542] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:19,542] [INFO] Target genome list was writen to GCF_030814315.1_ASM3081431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:19,558] [INFO] Task started: fastANI
[2024-01-25 18:55:19,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg722d7d27-0611-4481-91d4-0c75f6ded389/GCF_030814315.1_ASM3081431v1_genomic.fna.gz --refList GCF_030814315.1_ASM3081431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814315.1_ASM3081431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:29,887] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:29,890] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:55:29,891] [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_004341445.1	s__Baia soyae	89.4177	823	1064	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119485.1	s__Baia sp900119485	87.9054	810	1064	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107305.1	s__Baia sp900107305	87.361	790	1064	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:29,892] [INFO] GTDB search result was written to GCF_030814315.1_ASM3081431v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:29,892] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:29,894] [INFO] DFAST_QC result json was written to GCF_030814315.1_ASM3081431v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:29,894] [INFO] DFAST_QC completed!
[2024-01-25 18:55:29,894] [INFO] Total running time: 0h0m54s