[2023-06-19 07:29:23,328] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:29:23,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:29:23,331] [INFO] DQC Reference Directory: /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference
[2023-06-19 07:29:24,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:29:24,483] [INFO] Task started: Prodigal
[2023-06-19 07:29:24,483] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8dfb6a2-dd1e-4b43-a0a4-90fc1d806a6f/GCA_018065705.1_ASM1806570v1_genomic.fna.gz | prodigal -d GCA_018065705.1_ASM1806570v1_genomic.fna/cds.fna -a GCA_018065705.1_ASM1806570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:29:27,036] [INFO] Task succeeded: Prodigal
[2023-06-19 07:29:27,036] [INFO] Task started: HMMsearch
[2023-06-19 07:29:27,036] [INFO] Running command: hmmsearch --tblout GCA_018065705.1_ASM1806570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/reference_markers.hmm GCA_018065705.1_ASM1806570v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:29:27,182] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:29:27,183] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8dfb6a2-dd1e-4b43-a0a4-90fc1d806a6f/GCA_018065705.1_ASM1806570v1_genomic.fna.gz]
[2023-06-19 07:29:27,200] [INFO] Query marker FASTA was written to GCA_018065705.1_ASM1806570v1_genomic.fna/markers.fasta
[2023-06-19 07:29:27,200] [INFO] Task started: Blastn
[2023-06-19 07:29:27,200] [INFO] Running command: blastn -query GCA_018065705.1_ASM1806570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/reference_markers.fasta -out GCA_018065705.1_ASM1806570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:29:27,760] [INFO] Task succeeded: Blastn
[2023-06-19 07:29:27,764] [INFO] Selected 10 target genomes.
[2023-06-19 07:29:27,764] [INFO] Target genome list was writen to GCA_018065705.1_ASM1806570v1_genomic.fna/target_genomes.txt
[2023-06-19 07:29:27,765] [INFO] Task started: fastANI
[2023-06-19 07:29:27,765] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8dfb6a2-dd1e-4b43-a0a4-90fc1d806a6f/GCA_018065705.1_ASM1806570v1_genomic.fna.gz --refList GCA_018065705.1_ASM1806570v1_genomic.fna/target_genomes.txt --output GCA_018065705.1_ASM1806570v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:29:33,465] [INFO] Task succeeded: fastANI
[2023-06-19 07:29:33,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:29:33,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:29:33,467] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:29:33,468] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 07:29:33,468] [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
--------------------------------------------------------------------------------
[2023-06-19 07:29:33,469] [INFO] DFAST Taxonomy check result was written to GCA_018065705.1_ASM1806570v1_genomic.fna/tc_result.tsv
[2023-06-19 07:29:33,470] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:29:33,470] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:29:33,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/checkm_data
[2023-06-19 07:29:33,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:29:33,492] [INFO] Task started: CheckM
[2023-06-19 07:29:33,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018065705.1_ASM1806570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018065705.1_ASM1806570v1_genomic.fna/checkm_input GCA_018065705.1_ASM1806570v1_genomic.fna/checkm_result
[2023-06-19 07:29:48,482] [INFO] Task succeeded: CheckM
[2023-06-19 07:29:48,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.51%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:29:48,501] [INFO] ===== Completeness check finished =====
[2023-06-19 07:29:48,501] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:29:48,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018065705.1_ASM1806570v1_genomic.fna/markers.fasta)
[2023-06-19 07:29:48,502] [INFO] Task started: Blastn
[2023-06-19 07:29:48,502] [INFO] Running command: blastn -query GCA_018065705.1_ASM1806570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge426698c-c091-457c-aef0-46f30a3b41d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018065705.1_ASM1806570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:29:49,298] [INFO] Task succeeded: Blastn
[2023-06-19 07:29:49,302] [INFO] Selected 24 target genomes.
[2023-06-19 07:29:49,302] [INFO] Target genome list was writen to GCA_018065705.1_ASM1806570v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:29:49,311] [INFO] Task started: fastANI
[2023-06-19 07:29:49,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8dfb6a2-dd1e-4b43-a0a4-90fc1d806a6f/GCA_018065705.1_ASM1806570v1_genomic.fna.gz --refList GCA_018065705.1_ASM1806570v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018065705.1_ASM1806570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:29:56,107] [INFO] Task succeeded: fastANI
[2023-06-19 07:29:56,109] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 07:29:56,109] [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
--------------------------------------------------------------------------------
[2023-06-19 07:29:56,111] [INFO] GTDB search result was written to GCA_018065705.1_ASM1806570v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:29:56,111] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:29:56,113] [INFO] DFAST_QC result json was written to GCA_018065705.1_ASM1806570v1_genomic.fna/dqc_result.json
[2023-06-19 07:29:56,114] [INFO] DFAST_QC completed!
[2023-06-19 07:29:56,114] [INFO] Total running time: 0h0m33s