[2023-06-29 11:51:53,253] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:51:53,257] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:51:53,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference
[2023-06-29 11:51:54,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:51:54,604] [INFO] Task started: Prodigal
[2023-06-29 11:51:54,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgecaa93b0-7ee5-4813-bf66-cf3bb194ee1a/GCA_015484775.1_ASM1548477v1_genomic.fna.gz | prodigal -d GCA_015484775.1_ASM1548477v1_genomic.fna/cds.fna -a GCA_015484775.1_ASM1548477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:52:10,808] [INFO] Task succeeded: Prodigal
[2023-06-29 11:52:10,809] [INFO] Task started: HMMsearch
[2023-06-29 11:52:10,809] [INFO] Running command: hmmsearch --tblout GCA_015484775.1_ASM1548477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/reference_markers.hmm GCA_015484775.1_ASM1548477v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:52:11,079] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:52:11,081] [INFO] Found 6/6 markers.
[2023-06-29 11:52:11,113] [INFO] Query marker FASTA was written to GCA_015484775.1_ASM1548477v1_genomic.fna/markers.fasta
[2023-06-29 11:52:11,114] [INFO] Task started: Blastn
[2023-06-29 11:52:11,114] [INFO] Running command: blastn -query GCA_015484775.1_ASM1548477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/reference_markers.fasta -out GCA_015484775.1_ASM1548477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:52:11,749] [INFO] Task succeeded: Blastn
[2023-06-29 11:52:11,754] [INFO] Selected 38 target genomes.
[2023-06-29 11:52:11,755] [INFO] Target genome list was writen to GCA_015484775.1_ASM1548477v1_genomic.fna/target_genomes.txt
[2023-06-29 11:52:11,776] [INFO] Task started: fastANI
[2023-06-29 11:52:11,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgecaa93b0-7ee5-4813-bf66-cf3bb194ee1a/GCA_015484775.1_ASM1548477v1_genomic.fna.gz --refList GCA_015484775.1_ASM1548477v1_genomic.fna/target_genomes.txt --output GCA_015484775.1_ASM1548477v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:52:42,405] [INFO] Task succeeded: fastANI
[2023-06-29 11:52:42,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:52:42,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:52:42,412] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:52:42,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:52:42,413] [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
Cesiribacter andamanensis	strain=AMV16	GCA_000348925.1	649507	649507	type	True	75.6743	54	846	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:52:42,415] [INFO] DFAST Taxonomy check result was written to GCA_015484775.1_ASM1548477v1_genomic.fna/tc_result.tsv
[2023-06-29 11:52:42,416] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:52:42,416] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:52:42,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/checkm_data
[2023-06-29 11:52:42,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:52:42,453] [INFO] Task started: CheckM
[2023-06-29 11:52:42,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015484775.1_ASM1548477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015484775.1_ASM1548477v1_genomic.fna/checkm_input GCA_015484775.1_ASM1548477v1_genomic.fna/checkm_result
[2023-06-29 11:53:28,777] [INFO] Task succeeded: CheckM
[2023-06-29 11:53:28,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:53:28,805] [INFO] ===== Completeness check finished =====
[2023-06-29 11:53:28,806] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:53:28,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015484775.1_ASM1548477v1_genomic.fna/markers.fasta)
[2023-06-29 11:53:28,807] [INFO] Task started: Blastn
[2023-06-29 11:53:28,807] [INFO] Running command: blastn -query GCA_015484775.1_ASM1548477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6554c02-1568-4072-8344-0d7f58104555/dqc_reference/reference_markers_gtdb.fasta -out GCA_015484775.1_ASM1548477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:53:29,568] [INFO] Task succeeded: Blastn
[2023-06-29 11:53:29,573] [INFO] Selected 32 target genomes.
[2023-06-29 11:53:29,573] [INFO] Target genome list was writen to GCA_015484775.1_ASM1548477v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:53:29,617] [INFO] Task started: fastANI
[2023-06-29 11:53:29,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgecaa93b0-7ee5-4813-bf66-cf3bb194ee1a/GCA_015484775.1_ASM1548477v1_genomic.fna.gz --refList GCA_015484775.1_ASM1548477v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015484775.1_ASM1548477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:53:52,632] [INFO] Task succeeded: fastANI
[2023-06-29 11:53:52,637] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 11:53:52,637] [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_015488485.1	s__S012-113 sp015488485	98.8345	753	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__S012-113	95.0	99.09	98.80	0.91	0.89	4	conclusive
--------------------------------------------------------------------------------
[2023-06-29 11:53:52,639] [INFO] GTDB search result was written to GCA_015484775.1_ASM1548477v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:53:52,640] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:53:52,643] [INFO] DFAST_QC result json was written to GCA_015484775.1_ASM1548477v1_genomic.fna/dqc_result.json
[2023-06-29 11:53:52,643] [INFO] DFAST_QC completed!
[2023-06-29 11:53:52,643] [INFO] Total running time: 0h1m59s