[2023-06-07 23:15:52,803] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:52,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:52,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference
[2023-06-07 23:15:54,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:54,143] [INFO] Task started: Prodigal
[2023-06-07 23:15:54,143] [INFO] Running command: gunzip -c /var/lib/cwl/stge54531c4-3d07-41b8-919a-43556b59ed2e/GCA_902514005.1_AG-319-N09_genomic.fna.gz | prodigal -d GCA_902514005.1_AG-319-N09_genomic.fna/cds.fna -a GCA_902514005.1_AG-319-N09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:15:55,699] [INFO] Task succeeded: Prodigal
[2023-06-07 23:15:55,700] [INFO] Task started: HMMsearch
[2023-06-07 23:15:55,700] [INFO] Running command: hmmsearch --tblout GCA_902514005.1_AG-319-N09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/reference_markers.hmm GCA_902514005.1_AG-319-N09_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:15:55,877] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:15:55,879] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge54531c4-3d07-41b8-919a-43556b59ed2e/GCA_902514005.1_AG-319-N09_genomic.fna.gz]
[2023-06-07 23:15:55,897] [INFO] Query marker FASTA was written to GCA_902514005.1_AG-319-N09_genomic.fna/markers.fasta
[2023-06-07 23:15:55,897] [INFO] Task started: Blastn
[2023-06-07 23:15:55,897] [INFO] Running command: blastn -query GCA_902514005.1_AG-319-N09_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/reference_markers.fasta -out GCA_902514005.1_AG-319-N09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:15:57,082] [INFO] Task succeeded: Blastn
[2023-06-07 23:15:57,088] [INFO] Selected 15 target genomes.
[2023-06-07 23:15:57,088] [INFO] Target genome list was writen to GCA_902514005.1_AG-319-N09_genomic.fna/target_genomes.txt
[2023-06-07 23:15:57,090] [INFO] Task started: fastANI
[2023-06-07 23:15:57,090] [INFO] Running command: fastANI --query /var/lib/cwl/stge54531c4-3d07-41b8-919a-43556b59ed2e/GCA_902514005.1_AG-319-N09_genomic.fna.gz --refList GCA_902514005.1_AG-319-N09_genomic.fna/target_genomes.txt --output GCA_902514005.1_AG-319-N09_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:16:05,296] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:05,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:16:05,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:16:05,300] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:16:05,300] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 23:16:05,300] [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
--------------------------------------------------------------------------------
[2023-06-07 23:16:05,303] [INFO] DFAST Taxonomy check result was written to GCA_902514005.1_AG-319-N09_genomic.fna/tc_result.tsv
[2023-06-07 23:16:05,304] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:16:05,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:16:05,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/checkm_data
[2023-06-07 23:16:05,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:16:05,322] [INFO] Task started: CheckM
[2023-06-07 23:16:05,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902514005.1_AG-319-N09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902514005.1_AG-319-N09_genomic.fna/checkm_input GCA_902514005.1_AG-319-N09_genomic.fna/checkm_result
[2023-06-07 23:16:18,123] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:18,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:18,143] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:18,143] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:18,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902514005.1_AG-319-N09_genomic.fna/markers.fasta)
[2023-06-07 23:16:18,144] [INFO] Task started: Blastn
[2023-06-07 23:16:18,144] [INFO] Running command: blastn -query GCA_902514005.1_AG-319-N09_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfa617f-69a8-4f05-a57e-2190e83d3992/dqc_reference/reference_markers_gtdb.fasta -out GCA_902514005.1_AG-319-N09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:18,749] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:18,754] [INFO] Selected 13 target genomes.
[2023-06-07 23:16:18,754] [INFO] Target genome list was writen to GCA_902514005.1_AG-319-N09_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:18,806] [INFO] Task started: fastANI
[2023-06-07 23:16:18,806] [INFO] Running command: fastANI --query /var/lib/cwl/stge54531c4-3d07-41b8-919a-43556b59ed2e/GCA_902514005.1_AG-319-N09_genomic.fna.gz --refList GCA_902514005.1_AG-319-N09_genomic.fna/target_genomes_gtdb.txt --output GCA_902514005.1_AG-319-N09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:16:23,545] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:23,549] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:16:23,549] [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_902560065.1	s__GCA-2719315 sp902560065	85.8703	102	187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	85.4892	167	187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:16:23,551] [INFO] GTDB search result was written to GCA_902514005.1_AG-319-N09_genomic.fna/result_gtdb.tsv
[2023-06-07 23:16:23,552] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:16:23,554] [INFO] DFAST_QC result json was written to GCA_902514005.1_AG-319-N09_genomic.fna/dqc_result.json
[2023-06-07 23:16:23,554] [INFO] DFAST_QC completed!
[2023-06-07 23:16:23,554] [INFO] Total running time: 0h0m31s