[2023-06-30 17:00:09,053] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:09,056] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:09,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference
[2023-06-30 17:00:10,322] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:10,323] [INFO] Task started: Prodigal
[2023-06-30 17:00:10,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5e8bc66-8756-4e54-8a93-29695b9269df/GCA_016932075.1_ASM1693207v1_genomic.fna.gz | prodigal -d GCA_016932075.1_ASM1693207v1_genomic.fna/cds.fna -a GCA_016932075.1_ASM1693207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:21,140] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:21,141] [INFO] Task started: HMMsearch
[2023-06-30 17:00:21,141] [INFO] Running command: hmmsearch --tblout GCA_016932075.1_ASM1693207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/reference_markers.hmm GCA_016932075.1_ASM1693207v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:21,443] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:21,444] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5e8bc66-8756-4e54-8a93-29695b9269df/GCA_016932075.1_ASM1693207v1_genomic.fna.gz]
[2023-06-30 17:00:21,487] [INFO] Query marker FASTA was written to GCA_016932075.1_ASM1693207v1_genomic.fna/markers.fasta
[2023-06-30 17:00:21,488] [INFO] Task started: Blastn
[2023-06-30 17:00:21,488] [INFO] Running command: blastn -query GCA_016932075.1_ASM1693207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/reference_markers.fasta -out GCA_016932075.1_ASM1693207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:22,129] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:22,133] [INFO] Selected 25 target genomes.
[2023-06-30 17:00:22,134] [INFO] Target genome list was writen to GCA_016932075.1_ASM1693207v1_genomic.fna/target_genomes.txt
[2023-06-30 17:00:22,139] [INFO] Task started: fastANI
[2023-06-30 17:00:22,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e8bc66-8756-4e54-8a93-29695b9269df/GCA_016932075.1_ASM1693207v1_genomic.fna.gz --refList GCA_016932075.1_ASM1693207v1_genomic.fna/target_genomes.txt --output GCA_016932075.1_ASM1693207v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:40,560] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:40,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:40,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:40,563] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:40,563] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:00:40,563] [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
--------------------------------------------------------------------------------
[2023-06-30 17:00:40,565] [INFO] DFAST Taxonomy check result was written to GCA_016932075.1_ASM1693207v1_genomic.fna/tc_result.tsv
[2023-06-30 17:00:40,566] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:40,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:40,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/checkm_data
[2023-06-30 17:00:40,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:40,611] [INFO] Task started: CheckM
[2023-06-30 17:00:40,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016932075.1_ASM1693207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016932075.1_ASM1693207v1_genomic.fna/checkm_input GCA_016932075.1_ASM1693207v1_genomic.fna/checkm_result
[2023-06-30 17:01:16,450] [INFO] Task succeeded: CheckM
[2023-06-30 17:01:16,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:01:16,476] [INFO] ===== Completeness check finished =====
[2023-06-30 17:01:16,477] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:01:16,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016932075.1_ASM1693207v1_genomic.fna/markers.fasta)
[2023-06-30 17:01:16,478] [INFO] Task started: Blastn
[2023-06-30 17:01:16,478] [INFO] Running command: blastn -query GCA_016932075.1_ASM1693207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86d61c49-d62f-43ac-92a4-3941fc5361e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_016932075.1_ASM1693207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:01:17,370] [INFO] Task succeeded: Blastn
[2023-06-30 17:01:17,375] [INFO] Selected 18 target genomes.
[2023-06-30 17:01:17,376] [INFO] Target genome list was writen to GCA_016932075.1_ASM1693207v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:01:17,387] [INFO] Task started: fastANI
[2023-06-30 17:01:17,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e8bc66-8756-4e54-8a93-29695b9269df/GCA_016932075.1_ASM1693207v1_genomic.fna.gz --refList GCA_016932075.1_ASM1693207v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016932075.1_ASM1693207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:28,544] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:28,550] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:01:28,550] [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_016932075.1	s__JAFGDP01 sp016932075	100.0	1228	1244	d__Bacteria;p__Fibrobacterota;c__Chitinivibrionia;o__Chitinivibrionales;f__Chitinispirillaceae;g__JAFGDP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016926315.1	s__JAFGDP01 sp016926315	76.9019	216	1244	d__Bacteria;p__Fibrobacterota;c__Chitinivibrionia;o__Chitinivibrionales;f__Chitinispirillaceae;g__JAFGDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888815.1	s__BOG-1184 sp903888815	76.6211	72	1244	d__Bacteria;p__Fibrobacterota;c__Chitinivibrionia;o__Chitinivibrionales;f__Chitinispirillaceae;g__BOG-1184	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:01:28,552] [INFO] GTDB search result was written to GCA_016932075.1_ASM1693207v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:28,553] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:28,555] [INFO] DFAST_QC result json was written to GCA_016932075.1_ASM1693207v1_genomic.fna/dqc_result.json
[2023-06-30 17:01:28,555] [INFO] DFAST_QC completed!
[2023-06-30 17:01:28,555] [INFO] Total running time: 0h1m20s