[2023-06-14 01:48:08,198] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:48:08,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:48:08,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference
[2023-06-14 01:48:09,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:48:09,525] [INFO] Task started: Prodigal
[2023-06-14 01:48:09,526] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe92e667-8c70-4485-ab7c-857c878135ed/GCA_022705765.1_ASM2270576v1_genomic.fna.gz | prodigal -d GCA_022705765.1_ASM2270576v1_genomic.fna/cds.fna -a GCA_022705765.1_ASM2270576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:48:11,863] [INFO] Task succeeded: Prodigal
[2023-06-14 01:48:11,864] [INFO] Task started: HMMsearch
[2023-06-14 01:48:11,864] [INFO] Running command: hmmsearch --tblout GCA_022705765.1_ASM2270576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/reference_markers.hmm GCA_022705765.1_ASM2270576v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:48:12,064] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:48:12,066] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe92e667-8c70-4485-ab7c-857c878135ed/GCA_022705765.1_ASM2270576v1_genomic.fna.gz]
[2023-06-14 01:48:12,082] [INFO] Query marker FASTA was written to GCA_022705765.1_ASM2270576v1_genomic.fna/markers.fasta
[2023-06-14 01:48:12,083] [INFO] Task started: Blastn
[2023-06-14 01:48:12,083] [INFO] Running command: blastn -query GCA_022705765.1_ASM2270576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/reference_markers.fasta -out GCA_022705765.1_ASM2270576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:12,635] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:12,640] [INFO] Selected 5 target genomes.
[2023-06-14 01:48:12,640] [INFO] Target genome list was writen to GCA_022705765.1_ASM2270576v1_genomic.fna/target_genomes.txt
[2023-06-14 01:48:12,642] [INFO] Task started: fastANI
[2023-06-14 01:48:12,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe92e667-8c70-4485-ab7c-857c878135ed/GCA_022705765.1_ASM2270576v1_genomic.fna.gz --refList GCA_022705765.1_ASM2270576v1_genomic.fna/target_genomes.txt --output GCA_022705765.1_ASM2270576v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:48:15,048] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:15,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:48:15,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:48:15,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:48:15,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:48:15,051] [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
--------------------------------------------------------------------------------
[2023-06-14 01:48:15,053] [INFO] DFAST Taxonomy check result was written to GCA_022705765.1_ASM2270576v1_genomic.fna/tc_result.tsv
[2023-06-14 01:48:15,053] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:48:15,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:48:15,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/checkm_data
[2023-06-14 01:48:15,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:48:15,073] [INFO] Task started: CheckM
[2023-06-14 01:48:15,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022705765.1_ASM2270576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022705765.1_ASM2270576v1_genomic.fna/checkm_input GCA_022705765.1_ASM2270576v1_genomic.fna/checkm_result
[2023-06-14 01:48:30,072] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:30,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.24%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:30,093] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:30,093] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:30,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022705765.1_ASM2270576v1_genomic.fna/markers.fasta)
[2023-06-14 01:48:30,094] [INFO] Task started: Blastn
[2023-06-14 01:48:30,094] [INFO] Running command: blastn -query GCA_022705765.1_ASM2270576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54044333-2728-48b7-a297-7643d2152e73/dqc_reference/reference_markers_gtdb.fasta -out GCA_022705765.1_ASM2270576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:30,904] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:30,909] [INFO] Selected 16 target genomes.
[2023-06-14 01:48:30,909] [INFO] Target genome list was writen to GCA_022705765.1_ASM2270576v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:30,957] [INFO] Task started: fastANI
[2023-06-14 01:48:30,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe92e667-8c70-4485-ab7c-857c878135ed/GCA_022705765.1_ASM2270576v1_genomic.fna.gz --refList GCA_022705765.1_ASM2270576v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022705765.1_ASM2270576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:34,070] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:34,076] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:48:34,076] [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_903840015.1	s__UBA5232 sp903840015	95.887	150	177	d__Bacteria;p__Patescibacteria;c__Dojkabacteria;o__SC72;f__SC72;g__UBA5232	95.0	99.77	99.71	0.96	0.95	5	conclusive
--------------------------------------------------------------------------------
[2023-06-14 01:48:34,079] [INFO] GTDB search result was written to GCA_022705765.1_ASM2270576v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:34,080] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:34,083] [INFO] DFAST_QC result json was written to GCA_022705765.1_ASM2270576v1_genomic.fna/dqc_result.json
[2023-06-14 01:48:34,084] [INFO] DFAST_QC completed!
[2023-06-14 01:48:34,084] [INFO] Total running time: 0h0m26s