[2023-06-17 09:46:41,262] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:46:41,265] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:46:41,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference
[2023-06-17 09:46:43,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:46:43,335] [INFO] Task started: Prodigal
[2023-06-17 09:46:43,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgb159e5f6-4760-4938-a0d3-8180649feab3/GCA_013330865.1_ASM1333086v1_genomic.fna.gz | prodigal -d GCA_013330865.1_ASM1333086v1_genomic.fna/cds.fna -a GCA_013330865.1_ASM1333086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:46:50,770] [INFO] Task succeeded: Prodigal
[2023-06-17 09:46:50,771] [INFO] Task started: HMMsearch
[2023-06-17 09:46:50,771] [INFO] Running command: hmmsearch --tblout GCA_013330865.1_ASM1333086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/reference_markers.hmm GCA_013330865.1_ASM1333086v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:46:50,951] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:46:50,953] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb159e5f6-4760-4938-a0d3-8180649feab3/GCA_013330865.1_ASM1333086v1_genomic.fna.gz]
[2023-06-17 09:46:50,987] [INFO] Query marker FASTA was written to GCA_013330865.1_ASM1333086v1_genomic.fna/markers.fasta
[2023-06-17 09:46:50,988] [INFO] Task started: Blastn
[2023-06-17 09:46:50,988] [INFO] Running command: blastn -query GCA_013330865.1_ASM1333086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/reference_markers.fasta -out GCA_013330865.1_ASM1333086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:46:51,534] [INFO] Task succeeded: Blastn
[2023-06-17 09:46:51,538] [INFO] Selected 8 target genomes.
[2023-06-17 09:46:51,538] [INFO] Target genome list was writen to GCA_013330865.1_ASM1333086v1_genomic.fna/target_genomes.txt
[2023-06-17 09:46:51,540] [INFO] Task started: fastANI
[2023-06-17 09:46:51,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgb159e5f6-4760-4938-a0d3-8180649feab3/GCA_013330865.1_ASM1333086v1_genomic.fna.gz --refList GCA_013330865.1_ASM1333086v1_genomic.fna/target_genomes.txt --output GCA_013330865.1_ASM1333086v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:46:56,188] [INFO] Task succeeded: fastANI
[2023-06-17 09:46:56,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:46:56,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:46:56,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:46:56,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:46:56,214] [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
--------------------------------------------------------------------------------
[2023-06-17 09:46:56,216] [INFO] DFAST Taxonomy check result was written to GCA_013330865.1_ASM1333086v1_genomic.fna/tc_result.tsv
[2023-06-17 09:46:56,217] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:46:56,217] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:46:56,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/checkm_data
[2023-06-17 09:46:56,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:46:56,240] [INFO] Task started: CheckM
[2023-06-17 09:46:56,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013330865.1_ASM1333086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013330865.1_ASM1333086v1_genomic.fna/checkm_input GCA_013330865.1_ASM1333086v1_genomic.fna/checkm_result
[2023-06-17 09:47:22,209] [INFO] Task succeeded: CheckM
[2023-06-17 09:47:22,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:47:22,229] [INFO] ===== Completeness check finished =====
[2023-06-17 09:47:22,229] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:47:22,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013330865.1_ASM1333086v1_genomic.fna/markers.fasta)
[2023-06-17 09:47:22,230] [INFO] Task started: Blastn
[2023-06-17 09:47:22,230] [INFO] Running command: blastn -query GCA_013330865.1_ASM1333086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc09d2fd7-5e65-460b-b2bf-99dfe4ac7927/dqc_reference/reference_markers_gtdb.fasta -out GCA_013330865.1_ASM1333086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:47:22,953] [INFO] Task succeeded: Blastn
[2023-06-17 09:47:22,980] [INFO] Selected 8 target genomes.
[2023-06-17 09:47:22,981] [INFO] Target genome list was writen to GCA_013330865.1_ASM1333086v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:47:22,988] [INFO] Task started: fastANI
[2023-06-17 09:47:22,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgb159e5f6-4760-4938-a0d3-8180649feab3/GCA_013330865.1_ASM1333086v1_genomic.fna.gz --refList GCA_013330865.1_ASM1333086v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013330865.1_ASM1333086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:47:26,061] [INFO] Task succeeded: fastANI
[2023-06-17 09:47:26,066] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:47:26,066] [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_013330825.1	s__GW2011-AR11 sp12027u	99.3503	303	370	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR4;g__GW2011-AR11	95.0	99.09	98.49	0.82	0.78	7	conclusive
--------------------------------------------------------------------------------
[2023-06-17 09:47:26,068] [INFO] GTDB search result was written to GCA_013330865.1_ASM1333086v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:47:26,069] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:47:26,072] [INFO] DFAST_QC result json was written to GCA_013330865.1_ASM1333086v1_genomic.fna/dqc_result.json
[2023-06-17 09:47:26,072] [INFO] DFAST_QC completed!
[2023-06-17 09:47:26,072] [INFO] Total running time: 0h0m45s