[2023-06-13 00:09:18,690] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:09:18,696] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:09:18,696] [INFO] DQC Reference Directory: /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference
[2023-06-13 00:09:20,003] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:09:20,004] [INFO] Task started: Prodigal
[2023-06-13 00:09:20,004] [INFO] Running command: gunzip -c /var/lib/cwl/stga09065fc-6e07-48dd-bcf2-3781ad5788ff/GCA_022749835.1_ASM2274983v1_genomic.fna.gz | prodigal -d GCA_022749835.1_ASM2274983v1_genomic.fna/cds.fna -a GCA_022749835.1_ASM2274983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:09:27,666] [INFO] Task succeeded: Prodigal
[2023-06-13 00:09:27,667] [INFO] Task started: HMMsearch
[2023-06-13 00:09:27,667] [INFO] Running command: hmmsearch --tblout GCA_022749835.1_ASM2274983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/reference_markers.hmm GCA_022749835.1_ASM2274983v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:09:27,892] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:09:27,893] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga09065fc-6e07-48dd-bcf2-3781ad5788ff/GCA_022749835.1_ASM2274983v1_genomic.fna.gz]
[2023-06-13 00:09:27,932] [INFO] Query marker FASTA was written to GCA_022749835.1_ASM2274983v1_genomic.fna/markers.fasta
[2023-06-13 00:09:27,933] [INFO] Task started: Blastn
[2023-06-13 00:09:27,933] [INFO] Running command: blastn -query GCA_022749835.1_ASM2274983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/reference_markers.fasta -out GCA_022749835.1_ASM2274983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:28,434] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:28,443] [INFO] Selected 5 target genomes.
[2023-06-13 00:09:28,443] [INFO] Target genome list was writen to GCA_022749835.1_ASM2274983v1_genomic.fna/target_genomes.txt
[2023-06-13 00:09:28,446] [INFO] Task started: fastANI
[2023-06-13 00:09:28,446] [INFO] Running command: fastANI --query /var/lib/cwl/stga09065fc-6e07-48dd-bcf2-3781ad5788ff/GCA_022749835.1_ASM2274983v1_genomic.fna.gz --refList GCA_022749835.1_ASM2274983v1_genomic.fna/target_genomes.txt --output GCA_022749835.1_ASM2274983v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:09:32,127] [INFO] Task succeeded: fastANI
[2023-06-13 00:09:32,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:09:32,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:09:32,131] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:09:32,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:09:32,131] [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
--------------------------------------------------------------------------------
[2023-06-13 00:09:32,134] [INFO] DFAST Taxonomy check result was written to GCA_022749835.1_ASM2274983v1_genomic.fna/tc_result.tsv
[2023-06-13 00:09:32,139] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:09:32,139] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:09:32,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/checkm_data
[2023-06-13 00:09:32,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:09:32,172] [INFO] Task started: CheckM
[2023-06-13 00:09:32,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022749835.1_ASM2274983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022749835.1_ASM2274983v1_genomic.fna/checkm_input GCA_022749835.1_ASM2274983v1_genomic.fna/checkm_result
[2023-06-13 00:09:59,130] [INFO] Task succeeded: CheckM
[2023-06-13 00:09:59,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.90%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 00:09:59,176] [INFO] ===== Completeness check finished =====
[2023-06-13 00:09:59,177] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:09:59,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022749835.1_ASM2274983v1_genomic.fna/markers.fasta)
[2023-06-13 00:09:59,178] [INFO] Task started: Blastn
[2023-06-13 00:09:59,178] [INFO] Running command: blastn -query GCA_022749835.1_ASM2274983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36a3445-d15e-45ba-a1a1-fd53c00e06f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022749835.1_ASM2274983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:59,646] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:59,652] [INFO] Selected 10 target genomes.
[2023-06-13 00:09:59,652] [INFO] Target genome list was writen to GCA_022749835.1_ASM2274983v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:09:59,659] [INFO] Task started: fastANI
[2023-06-13 00:09:59,659] [INFO] Running command: fastANI --query /var/lib/cwl/stga09065fc-6e07-48dd-bcf2-3781ad5788ff/GCA_022749835.1_ASM2274983v1_genomic.fna.gz --refList GCA_022749835.1_ASM2274983v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022749835.1_ASM2274983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:04,454] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:04,459] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 00:10:04,460] [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_013290045.1	s__UBA184 sp013290045	78.1803	137	410	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503985.1	s__UBA184 sp002503985	77.9006	97	410	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044425.1	s__UBA184 sp013044425	77.4912	61	410	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495185.1	s__UBA184 sp002495185	77.4729	98	410	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:04,462] [INFO] GTDB search result was written to GCA_022749835.1_ASM2274983v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:04,474] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:04,482] [INFO] DFAST_QC result json was written to GCA_022749835.1_ASM2274983v1_genomic.fna/dqc_result.json
[2023-06-13 00:10:04,482] [INFO] DFAST_QC completed!
[2023-06-13 00:10:04,483] [INFO] Total running time: 0h0m46s