[2023-06-28 09:29:07,126] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:29:07,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:29:07,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference
[2023-06-28 09:29:08,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:29:08,430] [INFO] Task started: Prodigal
[2023-06-28 09:29:08,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d0f04c0-ca0d-4e57-8a27-c31687ffd60d/GCA_017607915.1_ASM1760791v1_genomic.fna.gz | prodigal -d GCA_017607915.1_ASM1760791v1_genomic.fna/cds.fna -a GCA_017607915.1_ASM1760791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:29:10,907] [INFO] Task succeeded: Prodigal
[2023-06-28 09:29:10,907] [INFO] Task started: HMMsearch
[2023-06-28 09:29:10,908] [INFO] Running command: hmmsearch --tblout GCA_017607915.1_ASM1760791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/reference_markers.hmm GCA_017607915.1_ASM1760791v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:29:11,085] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:29:11,086] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1d0f04c0-ca0d-4e57-8a27-c31687ffd60d/GCA_017607915.1_ASM1760791v1_genomic.fna.gz]
[2023-06-28 09:29:11,103] [INFO] Query marker FASTA was written to GCA_017607915.1_ASM1760791v1_genomic.fna/markers.fasta
[2023-06-28 09:29:11,104] [INFO] Task started: Blastn
[2023-06-28 09:29:11,104] [INFO] Running command: blastn -query GCA_017607915.1_ASM1760791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/reference_markers.fasta -out GCA_017607915.1_ASM1760791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:29:12,023] [INFO] Task succeeded: Blastn
[2023-06-28 09:29:12,027] [INFO] Selected 10 target genomes.
[2023-06-28 09:29:12,028] [INFO] Target genome list was writen to GCA_017607915.1_ASM1760791v1_genomic.fna/target_genomes.txt
[2023-06-28 09:29:12,068] [INFO] Task started: fastANI
[2023-06-28 09:29:12,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0f04c0-ca0d-4e57-8a27-c31687ffd60d/GCA_017607915.1_ASM1760791v1_genomic.fna.gz --refList GCA_017607915.1_ASM1760791v1_genomic.fna/target_genomes.txt --output GCA_017607915.1_ASM1760791v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:29:16,503] [INFO] Task succeeded: fastANI
[2023-06-28 09:29:16,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:29:16,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:29:16,505] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:29:16,505] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:29:16,505] [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
--------------------------------------------------------------------------------
[2023-06-28 09:29:16,514] [INFO] DFAST Taxonomy check result was written to GCA_017607915.1_ASM1760791v1_genomic.fna/tc_result.tsv
[2023-06-28 09:29:16,515] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:29:16,515] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:29:16,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/checkm_data
[2023-06-28 09:29:16,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:29:16,535] [INFO] Task started: CheckM
[2023-06-28 09:29:16,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017607915.1_ASM1760791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017607915.1_ASM1760791v1_genomic.fna/checkm_input GCA_017607915.1_ASM1760791v1_genomic.fna/checkm_result
[2023-06-28 09:29:32,010] [INFO] Task succeeded: CheckM
[2023-06-28 09:29:32,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 20.83%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:29:32,032] [INFO] ===== Completeness check finished =====
[2023-06-28 09:29:32,032] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:29:32,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017607915.1_ASM1760791v1_genomic.fna/markers.fasta)
[2023-06-28 09:29:32,033] [INFO] Task started: Blastn
[2023-06-28 09:29:32,033] [INFO] Running command: blastn -query GCA_017607915.1_ASM1760791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc75b9b2-40e1-4ed1-a887-6a8ca9481197/dqc_reference/reference_markers_gtdb.fasta -out GCA_017607915.1_ASM1760791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:29:32,752] [INFO] Task succeeded: Blastn
[2023-06-28 09:29:32,756] [INFO] Selected 14 target genomes.
[2023-06-28 09:29:32,756] [INFO] Target genome list was writen to GCA_017607915.1_ASM1760791v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:29:32,762] [INFO] Task started: fastANI
[2023-06-28 09:29:32,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0f04c0-ca0d-4e57-8a27-c31687ffd60d/GCA_017607915.1_ASM1760791v1_genomic.fna.gz --refList GCA_017607915.1_ASM1760791v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017607915.1_ASM1760791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:29:36,358] [INFO] Task succeeded: fastANI
[2023-06-28 09:29:36,362] [INFO] Found 2 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 09:29:36,362] [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_017609465.1	s__JAFCDX01 sp017609465	99.4715	194	417	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__JAFCDX01;g__JAFCDX01	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_017609525.1	s__JAFCDT01 sp017609525	97.589	65	417	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__JACPNG01;g__JAFCDT01	95.0	N/A	N/A	N/A	N/A	1	inconclusive
--------------------------------------------------------------------------------
[2023-06-28 09:29:36,364] [INFO] GTDB search result was written to GCA_017607915.1_ASM1760791v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:29:36,364] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:29:36,366] [INFO] DFAST_QC result json was written to GCA_017607915.1_ASM1760791v1_genomic.fna/dqc_result.json
[2023-06-28 09:29:36,366] [INFO] DFAST_QC completed!
[2023-06-28 09:29:36,367] [INFO] Total running time: 0h0m29s