[2023-06-27 22:09:49,541] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:09:49,544] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:09:49,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference
[2023-06-27 22:09:51,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:09:51,548] [INFO] Task started: Prodigal
[2023-06-27 22:09:51,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg5787c24c-fa02-48a8-baea-0072fce408b4/GCA_026396205.1_ASM2639620v1_genomic.fna.gz | prodigal -d GCA_026396205.1_ASM2639620v1_genomic.fna/cds.fna -a GCA_026396205.1_ASM2639620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:09:55,323] [INFO] Task succeeded: Prodigal
[2023-06-27 22:09:55,324] [INFO] Task started: HMMsearch
[2023-06-27 22:09:55,324] [INFO] Running command: hmmsearch --tblout GCA_026396205.1_ASM2639620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/reference_markers.hmm GCA_026396205.1_ASM2639620v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:09:55,548] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:09:55,550] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5787c24c-fa02-48a8-baea-0072fce408b4/GCA_026396205.1_ASM2639620v1_genomic.fna.gz]
[2023-06-27 22:09:55,567] [INFO] Query marker FASTA was written to GCA_026396205.1_ASM2639620v1_genomic.fna/markers.fasta
[2023-06-27 22:09:55,568] [INFO] Task started: Blastn
[2023-06-27 22:09:55,568] [INFO] Running command: blastn -query GCA_026396205.1_ASM2639620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/reference_markers.fasta -out GCA_026396205.1_ASM2639620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:09:56,578] [INFO] Task succeeded: Blastn
[2023-06-27 22:09:56,583] [INFO] Selected 15 target genomes.
[2023-06-27 22:09:56,584] [INFO] Target genome list was writen to GCA_026396205.1_ASM2639620v1_genomic.fna/target_genomes.txt
[2023-06-27 22:09:56,592] [INFO] Task started: fastANI
[2023-06-27 22:09:56,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg5787c24c-fa02-48a8-baea-0072fce408b4/GCA_026396205.1_ASM2639620v1_genomic.fna.gz --refList GCA_026396205.1_ASM2639620v1_genomic.fna/target_genomes.txt --output GCA_026396205.1_ASM2639620v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:10:06,747] [INFO] Task succeeded: fastANI
[2023-06-27 22:10:06,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:10:06,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:10:06,750] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:10:06,750] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 22:10:06,751] [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
--------------------------------------------------------------------------------
[2023-06-27 22:10:06,753] [INFO] DFAST Taxonomy check result was written to GCA_026396205.1_ASM2639620v1_genomic.fna/tc_result.tsv
[2023-06-27 22:10:06,754] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:10:06,754] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:10:06,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/checkm_data
[2023-06-27 22:10:06,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:10:06,773] [INFO] Task started: CheckM
[2023-06-27 22:10:06,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026396205.1_ASM2639620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026396205.1_ASM2639620v1_genomic.fna/checkm_input GCA_026396205.1_ASM2639620v1_genomic.fna/checkm_result
[2023-06-27 22:10:24,965] [INFO] Task succeeded: CheckM
[2023-06-27 22:10:24,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:10:24,987] [INFO] ===== Completeness check finished =====
[2023-06-27 22:10:24,987] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:10:24,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026396205.1_ASM2639620v1_genomic.fna/markers.fasta)
[2023-06-27 22:10:24,988] [INFO] Task started: Blastn
[2023-06-27 22:10:24,988] [INFO] Running command: blastn -query GCA_026396205.1_ASM2639620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6ca14f-f2ec-442c-8bdd-78493a2df495/dqc_reference/reference_markers_gtdb.fasta -out GCA_026396205.1_ASM2639620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:10:25,736] [INFO] Task succeeded: Blastn
[2023-06-27 22:10:25,741] [INFO] Selected 19 target genomes.
[2023-06-27 22:10:25,741] [INFO] Target genome list was writen to GCA_026396205.1_ASM2639620v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:10:25,751] [INFO] Task started: fastANI
[2023-06-27 22:10:25,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg5787c24c-fa02-48a8-baea-0072fce408b4/GCA_026396205.1_ASM2639620v1_genomic.fna.gz --refList GCA_026396205.1_ASM2639620v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026396205.1_ASM2639620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:10:31,373] [INFO] Task succeeded: fastANI
[2023-06-27 22:10:31,376] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:10:31,376] [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
--------------------------------------------------------------------------------
[2023-06-27 22:10:31,378] [INFO] GTDB search result was written to GCA_026396205.1_ASM2639620v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:10:31,379] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:10:31,381] [INFO] DFAST_QC result json was written to GCA_026396205.1_ASM2639620v1_genomic.fna/dqc_result.json
[2023-06-27 22:10:31,382] [INFO] DFAST_QC completed!
[2023-06-27 22:10:31,382] [INFO] Total running time: 0h0m42s