[2023-06-28 02:37:15,160] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:37:15,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:37:15,163] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference
[2023-06-28 02:37:16,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:37:16,384] [INFO] Task started: Prodigal
[2023-06-28 02:37:16,384] [INFO] Running command: gunzip -c /var/lib/cwl/stge34ac68f-d166-4c3d-bdb3-71e4c5804e29/GCA_017539425.1_ASM1753942v1_genomic.fna.gz | prodigal -d GCA_017539425.1_ASM1753942v1_genomic.fna/cds.fna -a GCA_017539425.1_ASM1753942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:37:21,534] [INFO] Task succeeded: Prodigal
[2023-06-28 02:37:21,535] [INFO] Task started: HMMsearch
[2023-06-28 02:37:21,535] [INFO] Running command: hmmsearch --tblout GCA_017539425.1_ASM1753942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/reference_markers.hmm GCA_017539425.1_ASM1753942v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:37:21,782] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:37:21,784] [INFO] Found 6/6 markers.
[2023-06-28 02:37:21,810] [INFO] Query marker FASTA was written to GCA_017539425.1_ASM1753942v1_genomic.fna/markers.fasta
[2023-06-28 02:37:21,811] [INFO] Task started: Blastn
[2023-06-28 02:37:21,811] [INFO] Running command: blastn -query GCA_017539425.1_ASM1753942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/reference_markers.fasta -out GCA_017539425.1_ASM1753942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:37:22,465] [INFO] Task succeeded: Blastn
[2023-06-28 02:37:22,469] [INFO] Selected 19 target genomes.
[2023-06-28 02:37:22,470] [INFO] Target genome list was writen to GCA_017539425.1_ASM1753942v1_genomic.fna/target_genomes.txt
[2023-06-28 02:37:22,474] [INFO] Task started: fastANI
[2023-06-28 02:37:22,474] [INFO] Running command: fastANI --query /var/lib/cwl/stge34ac68f-d166-4c3d-bdb3-71e4c5804e29/GCA_017539425.1_ASM1753942v1_genomic.fna.gz --refList GCA_017539425.1_ASM1753942v1_genomic.fna/target_genomes.txt --output GCA_017539425.1_ASM1753942v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:37:36,547] [INFO] Task succeeded: fastANI
[2023-06-28 02:37:36,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:37:36,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:37:36,550] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:37:36,550] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:37:36,551] [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
--------------------------------------------------------------------------------
[2023-06-28 02:37:36,553] [INFO] DFAST Taxonomy check result was written to GCA_017539425.1_ASM1753942v1_genomic.fna/tc_result.tsv
[2023-06-28 02:37:36,554] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:37:36,554] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:37:36,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/checkm_data
[2023-06-28 02:37:36,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:37:36,585] [INFO] Task started: CheckM
[2023-06-28 02:37:36,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017539425.1_ASM1753942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017539425.1_ASM1753942v1_genomic.fna/checkm_input GCA_017539425.1_ASM1753942v1_genomic.fna/checkm_result
[2023-06-28 02:37:59,266] [INFO] Task succeeded: CheckM
[2023-06-28 02:37:59,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:37:59,294] [INFO] ===== Completeness check finished =====
[2023-06-28 02:37:59,294] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:37:59,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017539425.1_ASM1753942v1_genomic.fna/markers.fasta)
[2023-06-28 02:37:59,295] [INFO] Task started: Blastn
[2023-06-28 02:37:59,295] [INFO] Running command: blastn -query GCA_017539425.1_ASM1753942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a23241-399c-4afb-bddc-190206a5ad07/dqc_reference/reference_markers_gtdb.fasta -out GCA_017539425.1_ASM1753942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:38:00,383] [INFO] Task succeeded: Blastn
[2023-06-28 02:38:00,388] [INFO] Selected 25 target genomes.
[2023-06-28 02:38:00,389] [INFO] Target genome list was writen to GCA_017539425.1_ASM1753942v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:38:00,404] [INFO] Task started: fastANI
[2023-06-28 02:38:00,405] [INFO] Running command: fastANI --query /var/lib/cwl/stge34ac68f-d166-4c3d-bdb3-71e4c5804e29/GCA_017539425.1_ASM1753942v1_genomic.fna.gz --refList GCA_017539425.1_ASM1753942v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017539425.1_ASM1753942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:38:10,071] [INFO] Task succeeded: fastANI
[2023-06-28 02:38:10,077] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 02:38:10,077] [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
GCA_017539425.1	s__RUG14240 sp017539425	100.0	625	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__RUG14240	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902797125.1	s__RUG14240 sp902797125	77.3281	88	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__RUG14240	95.0	97.75	97.34	0.81	0.75	4	-
--------------------------------------------------------------------------------
[2023-06-28 02:38:10,085] [INFO] GTDB search result was written to GCA_017539425.1_ASM1753942v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:38:10,087] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:38:10,089] [INFO] DFAST_QC result json was written to GCA_017539425.1_ASM1753942v1_genomic.fna/dqc_result.json
[2023-06-28 02:38:10,090] [INFO] DFAST_QC completed!
[2023-06-28 02:38:10,090] [INFO] Total running time: 0h0m55s