[2023-06-18 10:48:44,318] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:48:44,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:48:44,327] [INFO] DQC Reference Directory: /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference
[2023-06-18 10:48:46,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:48:46,142] [INFO] Task started: Prodigal
[2023-06-18 10:48:46,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg4652675f-9609-4dbb-8cee-80e7f2fee467/GCA_018901455.1_ASM1890145v1_genomic.fna.gz | prodigal -d GCA_018901455.1_ASM1890145v1_genomic.fna/cds.fna -a GCA_018901455.1_ASM1890145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:48:49,104] [INFO] Task succeeded: Prodigal
[2023-06-18 10:48:49,104] [INFO] Task started: HMMsearch
[2023-06-18 10:48:49,104] [INFO] Running command: hmmsearch --tblout GCA_018901455.1_ASM1890145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/reference_markers.hmm GCA_018901455.1_ASM1890145v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:48:49,339] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:48:49,342] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4652675f-9609-4dbb-8cee-80e7f2fee467/GCA_018901455.1_ASM1890145v1_genomic.fna.gz]
[2023-06-18 10:48:49,356] [INFO] Query marker FASTA was written to GCA_018901455.1_ASM1890145v1_genomic.fna/markers.fasta
[2023-06-18 10:48:49,356] [INFO] Task started: Blastn
[2023-06-18 10:48:49,356] [INFO] Running command: blastn -query GCA_018901455.1_ASM1890145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/reference_markers.fasta -out GCA_018901455.1_ASM1890145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:48:51,451] [INFO] Task succeeded: Blastn
[2023-06-18 10:48:51,457] [INFO] Selected 10 target genomes.
[2023-06-18 10:48:51,458] [INFO] Target genome list was writen to GCA_018901455.1_ASM1890145v1_genomic.fna/target_genomes.txt
[2023-06-18 10:48:51,461] [INFO] Task started: fastANI
[2023-06-18 10:48:51,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg4652675f-9609-4dbb-8cee-80e7f2fee467/GCA_018901455.1_ASM1890145v1_genomic.fna.gz --refList GCA_018901455.1_ASM1890145v1_genomic.fna/target_genomes.txt --output GCA_018901455.1_ASM1890145v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:48:57,990] [INFO] Task succeeded: fastANI
[2023-06-18 10:48:57,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:48:57,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:48:57,992] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:48:57,993] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:48:57,993] [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
--------------------------------------------------------------------------------
[2023-06-18 10:48:57,995] [INFO] DFAST Taxonomy check result was written to GCA_018901455.1_ASM1890145v1_genomic.fna/tc_result.tsv
[2023-06-18 10:48:57,998] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:48:57,998] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:48:57,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/checkm_data
[2023-06-18 10:48:58,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:48:58,014] [INFO] Task started: CheckM
[2023-06-18 10:48:58,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018901455.1_ASM1890145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018901455.1_ASM1890145v1_genomic.fna/checkm_input GCA_018901455.1_ASM1890145v1_genomic.fna/checkm_result
[2023-06-18 10:49:13,232] [INFO] Task succeeded: CheckM
[2023-06-18 10:49:13,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.40%
Contamintation: 5.24%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 10:49:13,259] [INFO] ===== Completeness check finished =====
[2023-06-18 10:49:13,259] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:49:13,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018901455.1_ASM1890145v1_genomic.fna/markers.fasta)
[2023-06-18 10:49:13,260] [INFO] Task started: Blastn
[2023-06-18 10:49:13,260] [INFO] Running command: blastn -query GCA_018901455.1_ASM1890145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd71f0c50-fd44-46b3-bae6-238a9a591698/dqc_reference/reference_markers_gtdb.fasta -out GCA_018901455.1_ASM1890145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:49:13,948] [INFO] Task succeeded: Blastn
[2023-06-18 10:49:13,952] [INFO] Selected 15 target genomes.
[2023-06-18 10:49:13,952] [INFO] Target genome list was writen to GCA_018901455.1_ASM1890145v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:49:14,029] [INFO] Task started: fastANI
[2023-06-18 10:49:14,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg4652675f-9609-4dbb-8cee-80e7f2fee467/GCA_018901455.1_ASM1890145v1_genomic.fna.gz --refList GCA_018901455.1_ASM1890145v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018901455.1_ASM1890145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:49:16,431] [INFO] Task succeeded: fastANI
[2023-06-18 10:49:16,436] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 10:49:16,436] [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_018826025.1	s__UBA8475 sp018826025	79.7263	87	148	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Portnoybacterales;f__GWB1-42-6;g__UBA8475	95.0	99.04	99.04	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-18 10:49:16,438] [INFO] GTDB search result was written to GCA_018901455.1_ASM1890145v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:49:16,439] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:49:16,443] [INFO] DFAST_QC result json was written to GCA_018901455.1_ASM1890145v1_genomic.fna/dqc_result.json
[2023-06-18 10:49:16,443] [INFO] DFAST_QC completed!
[2023-06-18 10:49:16,443] [INFO] Total running time: 0h0m32s