[2023-06-29 09:02:33,549] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:33,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:33,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference
[2023-06-29 09:02:34,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:34,993] [INFO] Task started: Prodigal
[2023-06-29 09:02:34,993] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb36bf21-1d89-47a2-812e-10716e6ac526/GCA_020348065.1_ASM2034806v1_genomic.fna.gz | prodigal -d GCA_020348065.1_ASM2034806v1_genomic.fna/cds.fna -a GCA_020348065.1_ASM2034806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:43,547] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:43,548] [INFO] Task started: HMMsearch
[2023-06-29 09:02:43,548] [INFO] Running command: hmmsearch --tblout GCA_020348065.1_ASM2034806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/reference_markers.hmm GCA_020348065.1_ASM2034806v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:43,819] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:43,820] [INFO] Found 6/6 markers.
[2023-06-29 09:02:43,858] [INFO] Query marker FASTA was written to GCA_020348065.1_ASM2034806v1_genomic.fna/markers.fasta
[2023-06-29 09:02:43,859] [INFO] Task started: Blastn
[2023-06-29 09:02:43,859] [INFO] Running command: blastn -query GCA_020348065.1_ASM2034806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/reference_markers.fasta -out GCA_020348065.1_ASM2034806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:44,506] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:44,532] [INFO] Selected 14 target genomes.
[2023-06-29 09:02:44,533] [INFO] Target genome list was writen to GCA_020348065.1_ASM2034806v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:44,536] [INFO] Task started: fastANI
[2023-06-29 09:02:44,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb36bf21-1d89-47a2-812e-10716e6ac526/GCA_020348065.1_ASM2034806v1_genomic.fna.gz --refList GCA_020348065.1_ASM2034806v1_genomic.fna/target_genomes.txt --output GCA_020348065.1_ASM2034806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:02:53,998] [INFO] Task succeeded: fastANI
[2023-06-29 09:02:53,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:02:53,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:02:54,000] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:02:54,000] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:02:54,000] [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
--------------------------------------------------------------------------------
[2023-06-29 09:02:54,002] [INFO] DFAST Taxonomy check result was written to GCA_020348065.1_ASM2034806v1_genomic.fna/tc_result.tsv
[2023-06-29 09:02:54,003] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:02:54,003] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:02:54,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/checkm_data
[2023-06-29 09:02:54,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:02:54,052] [INFO] Task started: CheckM
[2023-06-29 09:02:54,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020348065.1_ASM2034806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020348065.1_ASM2034806v1_genomic.fna/checkm_input GCA_020348065.1_ASM2034806v1_genomic.fna/checkm_result
[2023-06-29 09:03:24,244] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:24,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:24,269] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:24,269] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:24,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020348065.1_ASM2034806v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:24,270] [INFO] Task started: Blastn
[2023-06-29 09:03:24,270] [INFO] Running command: blastn -query GCA_020348065.1_ASM2034806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9203e2d-3a1f-4834-af11-eceefb9e86a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020348065.1_ASM2034806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:25,318] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:25,323] [INFO] Selected 30 target genomes.
[2023-06-29 09:03:25,324] [INFO] Target genome list was writen to GCA_020348065.1_ASM2034806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:25,359] [INFO] Task started: fastANI
[2023-06-29 09:03:25,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb36bf21-1d89-47a2-812e-10716e6ac526/GCA_020348065.1_ASM2034806v1_genomic.fna.gz --refList GCA_020348065.1_ASM2034806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020348065.1_ASM2034806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:03:42,217] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:42,219] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:03:42,219] [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
--------------------------------------------------------------------------------
[2023-06-29 09:03:42,222] [INFO] GTDB search result was written to GCA_020348065.1_ASM2034806v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:03:42,223] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:03:42,225] [INFO] DFAST_QC result json was written to GCA_020348065.1_ASM2034806v1_genomic.fna/dqc_result.json
[2023-06-29 09:03:42,226] [INFO] DFAST_QC completed!
[2023-06-29 09:03:42,226] [INFO] Total running time: 0h1m9s