[2023-06-13 08:07:30,337] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:30,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:30,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference
[2023-06-13 08:07:31,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:31,562] [INFO] Task started: Prodigal
[2023-06-13 08:07:31,563] [INFO] Running command: gunzip -c /var/lib/cwl/stga2cf8553-86a4-4203-a0bd-e80bdd20ff28/GCA_022708465.1_ASM2270846v1_genomic.fna.gz | prodigal -d GCA_022708465.1_ASM2270846v1_genomic.fna/cds.fna -a GCA_022708465.1_ASM2270846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:36,928] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:36,929] [INFO] Task started: HMMsearch
[2023-06-13 08:07:36,929] [INFO] Running command: hmmsearch --tblout GCA_022708465.1_ASM2270846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/reference_markers.hmm GCA_022708465.1_ASM2270846v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:37,094] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:37,095] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga2cf8553-86a4-4203-a0bd-e80bdd20ff28/GCA_022708465.1_ASM2270846v1_genomic.fna.gz]
[2023-06-13 08:07:37,113] [INFO] Query marker FASTA was written to GCA_022708465.1_ASM2270846v1_genomic.fna/markers.fasta
[2023-06-13 08:07:37,113] [INFO] Task started: Blastn
[2023-06-13 08:07:37,114] [INFO] Running command: blastn -query GCA_022708465.1_ASM2270846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/reference_markers.fasta -out GCA_022708465.1_ASM2270846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:37,668] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:37,671] [INFO] Selected 22 target genomes.
[2023-06-13 08:07:37,671] [INFO] Target genome list was writen to GCA_022708465.1_ASM2270846v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:37,675] [INFO] Task started: fastANI
[2023-06-13 08:07:37,676] [INFO] Running command: fastANI --query /var/lib/cwl/stga2cf8553-86a4-4203-a0bd-e80bdd20ff28/GCA_022708465.1_ASM2270846v1_genomic.fna.gz --refList GCA_022708465.1_ASM2270846v1_genomic.fna/target_genomes.txt --output GCA_022708465.1_ASM2270846v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:52,824] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:52,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:52,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:52,827] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:07:52,827] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 08:07:52,827] [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
--------------------------------------------------------------------------------
[2023-06-13 08:07:52,829] [INFO] DFAST Taxonomy check result was written to GCA_022708465.1_ASM2270846v1_genomic.fna/tc_result.tsv
[2023-06-13 08:07:52,830] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:52,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:52,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/checkm_data
[2023-06-13 08:07:52,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:52,850] [INFO] Task started: CheckM
[2023-06-13 08:07:52,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708465.1_ASM2270846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708465.1_ASM2270846v1_genomic.fna/checkm_input GCA_022708465.1_ASM2270846v1_genomic.fna/checkm_result
[2023-06-13 08:08:14,744] [INFO] Task succeeded: CheckM
[2023-06-13 08:08:14,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:08:14,759] [INFO] ===== Completeness check finished =====
[2023-06-13 08:08:14,759] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:08:14,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708465.1_ASM2270846v1_genomic.fna/markers.fasta)
[2023-06-13 08:08:14,759] [INFO] Task started: Blastn
[2023-06-13 08:08:14,759] [INFO] Running command: blastn -query GCA_022708465.1_ASM2270846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318034d0-3324-4592-9814-81120e9088e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708465.1_ASM2270846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:15,528] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:15,531] [INFO] Selected 17 target genomes.
[2023-06-13 08:08:15,531] [INFO] Target genome list was writen to GCA_022708465.1_ASM2270846v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:15,538] [INFO] Task started: fastANI
[2023-06-13 08:08:15,538] [INFO] Running command: fastANI --query /var/lib/cwl/stga2cf8553-86a4-4203-a0bd-e80bdd20ff28/GCA_022708465.1_ASM2270846v1_genomic.fna.gz --refList GCA_022708465.1_ASM2270846v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708465.1_ASM2270846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:23,562] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:23,566] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:08:23,567] [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_002069025.1	s__Enterocola sp002069025	99.5629	323	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Enterocola	95.0	98.76	98.76	0.63	0.63	2	conclusive
GCA_009930305.1	s__Enterocola sp009930305	91.4611	417	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Enterocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:08:23,568] [INFO] GTDB search result was written to GCA_022708465.1_ASM2270846v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:23,569] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:23,571] [INFO] DFAST_QC result json was written to GCA_022708465.1_ASM2270846v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:23,571] [INFO] DFAST_QC completed!
[2023-06-13 08:08:23,571] [INFO] Total running time: 0h0m53s