[2023-06-18 12:30:58,296] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:58,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:58,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference
[2023-06-18 12:30:59,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:59,643] [INFO] Task started: Prodigal
[2023-06-18 12:30:59,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c3b3cc5-a861-44b5-b5ba-a74c319c2eff/GCA_018063005.1_ASM1806300v1_genomic.fna.gz | prodigal -d GCA_018063005.1_ASM1806300v1_genomic.fna/cds.fna -a GCA_018063005.1_ASM1806300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:31:03,869] [INFO] Task succeeded: Prodigal
[2023-06-18 12:31:03,869] [INFO] Task started: HMMsearch
[2023-06-18 12:31:03,869] [INFO] Running command: hmmsearch --tblout GCA_018063005.1_ASM1806300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/reference_markers.hmm GCA_018063005.1_ASM1806300v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:31:04,080] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:31:04,081] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1c3b3cc5-a861-44b5-b5ba-a74c319c2eff/GCA_018063005.1_ASM1806300v1_genomic.fna.gz]
[2023-06-18 12:31:04,096] [INFO] Query marker FASTA was written to GCA_018063005.1_ASM1806300v1_genomic.fna/markers.fasta
[2023-06-18 12:31:04,096] [INFO] Task started: Blastn
[2023-06-18 12:31:04,097] [INFO] Running command: blastn -query GCA_018063005.1_ASM1806300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/reference_markers.fasta -out GCA_018063005.1_ASM1806300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:04,661] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:04,667] [INFO] Selected 6 target genomes.
[2023-06-18 12:31:04,667] [INFO] Target genome list was writen to GCA_018063005.1_ASM1806300v1_genomic.fna/target_genomes.txt
[2023-06-18 12:31:04,669] [INFO] Task started: fastANI
[2023-06-18 12:31:04,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3b3cc5-a861-44b5-b5ba-a74c319c2eff/GCA_018063005.1_ASM1806300v1_genomic.fna.gz --refList GCA_018063005.1_ASM1806300v1_genomic.fna/target_genomes.txt --output GCA_018063005.1_ASM1806300v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:31:08,559] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:08,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:31:08,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:31:08,562] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:31:08,562] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:31:08,563] [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 12:31:08,565] [INFO] DFAST Taxonomy check result was written to GCA_018063005.1_ASM1806300v1_genomic.fna/tc_result.tsv
[2023-06-18 12:31:08,566] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:31:08,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:31:08,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/checkm_data
[2023-06-18 12:31:08,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:31:08,590] [INFO] Task started: CheckM
[2023-06-18 12:31:08,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018063005.1_ASM1806300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018063005.1_ASM1806300v1_genomic.fna/checkm_input GCA_018063005.1_ASM1806300v1_genomic.fna/checkm_result
[2023-06-18 12:31:29,597] [INFO] Task succeeded: CheckM
[2023-06-18 12:31:29,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 9.72%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-18 12:31:29,635] [INFO] ===== Completeness check finished =====
[2023-06-18 12:31:29,635] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:31:29,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018063005.1_ASM1806300v1_genomic.fna/markers.fasta)
[2023-06-18 12:31:29,636] [INFO] Task started: Blastn
[2023-06-18 12:31:29,638] [INFO] Running command: blastn -query GCA_018063005.1_ASM1806300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24f47572-6d54-4d49-b3d1-02dd4b11b715/dqc_reference/reference_markers_gtdb.fasta -out GCA_018063005.1_ASM1806300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:30,403] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:30,408] [INFO] Selected 17 target genomes.
[2023-06-18 12:31:30,408] [INFO] Target genome list was writen to GCA_018063005.1_ASM1806300v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:31:30,472] [INFO] Task started: fastANI
[2023-06-18 12:31:30,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3b3cc5-a861-44b5-b5ba-a74c319c2eff/GCA_018063005.1_ASM1806300v1_genomic.fna.gz --refList GCA_018063005.1_ASM1806300v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018063005.1_ASM1806300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:34,525] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:34,530] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:31:34,530] [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_017992505.1	s__OLB19 sp017992505	99.3101	180	256	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA918;g__OLB19	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-18 12:31:34,533] [INFO] GTDB search result was written to GCA_018063005.1_ASM1806300v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:34,533] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:34,538] [INFO] DFAST_QC result json was written to GCA_018063005.1_ASM1806300v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:34,538] [INFO] DFAST_QC completed!
[2023-06-18 12:31:34,538] [INFO] Total running time: 0h0m36s