[2023-06-28 07:44:09,145] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:44:09,148] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:44:09,148] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference
[2023-06-28 07:44:10,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:44:10,426] [INFO] Task started: Prodigal
[2023-06-28 07:44:10,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg16d084dc-9b4f-4e88-b440-557956e27f39/GCA_002708245.1_ASM270824v1_genomic.fna.gz | prodigal -d GCA_002708245.1_ASM270824v1_genomic.fna/cds.fna -a GCA_002708245.1_ASM270824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:44:13,108] [INFO] Task succeeded: Prodigal
[2023-06-28 07:44:13,109] [INFO] Task started: HMMsearch
[2023-06-28 07:44:13,109] [INFO] Running command: hmmsearch --tblout GCA_002708245.1_ASM270824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/reference_markers.hmm GCA_002708245.1_ASM270824v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:44:13,330] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:44:13,331] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg16d084dc-9b4f-4e88-b440-557956e27f39/GCA_002708245.1_ASM270824v1_genomic.fna.gz]
[2023-06-28 07:44:13,349] [INFO] Query marker FASTA was written to GCA_002708245.1_ASM270824v1_genomic.fna/markers.fasta
[2023-06-28 07:44:13,350] [INFO] Task started: Blastn
[2023-06-28 07:44:13,350] [INFO] Running command: blastn -query GCA_002708245.1_ASM270824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/reference_markers.fasta -out GCA_002708245.1_ASM270824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:44:13,887] [INFO] Task succeeded: Blastn
[2023-06-28 07:44:13,892] [INFO] Selected 12 target genomes.
[2023-06-28 07:44:13,893] [INFO] Target genome list was writen to GCA_002708245.1_ASM270824v1_genomic.fna/target_genomes.txt
[2023-06-28 07:44:13,894] [INFO] Task started: fastANI
[2023-06-28 07:44:13,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d084dc-9b4f-4e88-b440-557956e27f39/GCA_002708245.1_ASM270824v1_genomic.fna.gz --refList GCA_002708245.1_ASM270824v1_genomic.fna/target_genomes.txt --output GCA_002708245.1_ASM270824v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:44:20,451] [INFO] Task succeeded: fastANI
[2023-06-28 07:44:20,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:44:20,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:44:20,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:44:20,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 07:44:20,454] [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 07:44:20,456] [INFO] DFAST Taxonomy check result was written to GCA_002708245.1_ASM270824v1_genomic.fna/tc_result.tsv
[2023-06-28 07:44:20,457] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:44:20,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:44:20,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/checkm_data
[2023-06-28 07:44:20,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:44:20,486] [INFO] Task started: CheckM
[2023-06-28 07:44:20,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708245.1_ASM270824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708245.1_ASM270824v1_genomic.fna/checkm_input GCA_002708245.1_ASM270824v1_genomic.fna/checkm_result
[2023-06-28 07:44:36,669] [INFO] Task succeeded: CheckM
[2023-06-28 07:44:36,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 07:44:36,696] [INFO] ===== Completeness check finished =====
[2023-06-28 07:44:36,697] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:44:36,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708245.1_ASM270824v1_genomic.fna/markers.fasta)
[2023-06-28 07:44:36,698] [INFO] Task started: Blastn
[2023-06-28 07:44:36,698] [INFO] Running command: blastn -query GCA_002708245.1_ASM270824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5288b2d-2fd8-417a-8f3a-f2c0cb0eb753/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708245.1_ASM270824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:44:37,388] [INFO] Task succeeded: Blastn
[2023-06-28 07:44:37,392] [INFO] Selected 15 target genomes.
[2023-06-28 07:44:37,392] [INFO] Target genome list was writen to GCA_002708245.1_ASM270824v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:44:37,446] [INFO] Task started: fastANI
[2023-06-28 07:44:37,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d084dc-9b4f-4e88-b440-557956e27f39/GCA_002708245.1_ASM270824v1_genomic.fna.gz --refList GCA_002708245.1_ASM270824v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708245.1_ASM270824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:44:43,766] [INFO] Task succeeded: fastANI
[2023-06-28 07:44:43,771] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:44:43,772] [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_002713285.1	s__SP256 sp002713285	79.6005	186	283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722215.1	s__SP256 sp002722215	78.313	126	283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.5748	129	283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	77.3894	97	283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:44:43,775] [INFO] GTDB search result was written to GCA_002708245.1_ASM270824v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:44:43,776] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:44:43,778] [INFO] DFAST_QC result json was written to GCA_002708245.1_ASM270824v1_genomic.fna/dqc_result.json
[2023-06-28 07:44:43,779] [INFO] DFAST_QC completed!
[2023-06-28 07:44:43,779] [INFO] Total running time: 0h0m35s