[2023-06-30 05:04:01,133] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:04:01,135] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:04:01,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference
[2023-06-30 05:04:02,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:04:02,317] [INFO] Task started: Prodigal
[2023-06-30 05:04:02,317] [INFO] Running command: gunzip -c /var/lib/cwl/stg285c9e7d-2b36-4a11-9919-041d71020c4e/GCA_024276335.1_ASM2427633v1_genomic.fna.gz | prodigal -d GCA_024276335.1_ASM2427633v1_genomic.fna/cds.fna -a GCA_024276335.1_ASM2427633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:04:10,708] [INFO] Task succeeded: Prodigal
[2023-06-30 05:04:10,709] [INFO] Task started: HMMsearch
[2023-06-30 05:04:10,709] [INFO] Running command: hmmsearch --tblout GCA_024276335.1_ASM2427633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/reference_markers.hmm GCA_024276335.1_ASM2427633v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:04:10,958] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:04:10,959] [INFO] Found 6/6 markers.
[2023-06-30 05:04:10,992] [INFO] Query marker FASTA was written to GCA_024276335.1_ASM2427633v1_genomic.fna/markers.fasta
[2023-06-30 05:04:10,992] [INFO] Task started: Blastn
[2023-06-30 05:04:10,992] [INFO] Running command: blastn -query GCA_024276335.1_ASM2427633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/reference_markers.fasta -out GCA_024276335.1_ASM2427633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:11,583] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:11,589] [INFO] Selected 25 target genomes.
[2023-06-30 05:04:11,589] [INFO] Target genome list was writen to GCA_024276335.1_ASM2427633v1_genomic.fna/target_genomes.txt
[2023-06-30 05:04:11,591] [INFO] Task started: fastANI
[2023-06-30 05:04:11,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg285c9e7d-2b36-4a11-9919-041d71020c4e/GCA_024276335.1_ASM2427633v1_genomic.fna.gz --refList GCA_024276335.1_ASM2427633v1_genomic.fna/target_genomes.txt --output GCA_024276335.1_ASM2427633v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:04:31,249] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:31,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:04:31,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:04:31,252] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:04:31,252] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:04:31,253] [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 05:04:31,255] [INFO] DFAST Taxonomy check result was written to GCA_024276335.1_ASM2427633v1_genomic.fna/tc_result.tsv
[2023-06-30 05:04:31,256] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:04:31,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:04:31,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/checkm_data
[2023-06-30 05:04:31,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:04:31,299] [INFO] Task started: CheckM
[2023-06-30 05:04:31,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024276335.1_ASM2427633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024276335.1_ASM2427633v1_genomic.fna/checkm_input GCA_024276335.1_ASM2427633v1_genomic.fna/checkm_result
[2023-06-30 05:05:01,139] [INFO] Task succeeded: CheckM
[2023-06-30 05:05:01,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 05:05:01,168] [INFO] ===== Completeness check finished =====
[2023-06-30 05:05:01,169] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:05:01,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024276335.1_ASM2427633v1_genomic.fna/markers.fasta)
[2023-06-30 05:05:01,169] [INFO] Task started: Blastn
[2023-06-30 05:05:01,169] [INFO] Running command: blastn -query GCA_024276335.1_ASM2427633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg402d950e-e661-4cbb-a402-a3d71a8ace7c/dqc_reference/reference_markers_gtdb.fasta -out GCA_024276335.1_ASM2427633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:05:01,964] [INFO] Task succeeded: Blastn
[2023-06-30 05:05:01,969] [INFO] Selected 23 target genomes.
[2023-06-30 05:05:01,969] [INFO] Target genome list was writen to GCA_024276335.1_ASM2427633v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:05:01,976] [INFO] Task started: fastANI
[2023-06-30 05:05:01,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg285c9e7d-2b36-4a11-9919-041d71020c4e/GCA_024276335.1_ASM2427633v1_genomic.fna.gz --refList GCA_024276335.1_ASM2427633v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024276335.1_ASM2427633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:05:16,501] [INFO] Task succeeded: fastANI
[2023-06-30 05:05:16,506] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:05:16,506] [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_013152135.1	s__JAADGX01 sp013152135	83.8538	503	854	d__Bacteria;p__Bacteroidota;c__SZUA-365;o__SZUA-365;f__JAADGX01;g__JAADGX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:05:16,509] [INFO] GTDB search result was written to GCA_024276335.1_ASM2427633v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:05:16,509] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:05:16,512] [INFO] DFAST_QC result json was written to GCA_024276335.1_ASM2427633v1_genomic.fna/dqc_result.json
[2023-06-30 05:05:16,512] [INFO] DFAST_QC completed!
[2023-06-30 05:05:16,512] [INFO] Total running time: 0h1m15s