[2023-06-04 18:00:15,752] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:15,755] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:15,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference
[2023-06-04 18:00:16,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:16,999] [INFO] Task started: Prodigal
[2023-06-04 18:00:16,999] [INFO] Running command: gunzip -c /var/lib/cwl/stgac51a922-8c19-4116-a959-052b36bde757/GCA_001004185.1_ASM100418v1_genomic.fna.gz | prodigal -d GCA_001004185.1_ASM100418v1_genomic.fna/cds.fna -a GCA_001004185.1_ASM100418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:19,165] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:19,166] [INFO] Task started: HMMsearch
[2023-06-04 18:00:19,166] [INFO] Running command: hmmsearch --tblout GCA_001004185.1_ASM100418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/reference_markers.hmm GCA_001004185.1_ASM100418v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:19,424] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:19,425] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgac51a922-8c19-4116-a959-052b36bde757/GCA_001004185.1_ASM100418v1_genomic.fna.gz]
[2023-06-04 18:00:19,436] [INFO] Query marker FASTA was written to GCA_001004185.1_ASM100418v1_genomic.fna/markers.fasta
[2023-06-04 18:00:19,437] [INFO] Task started: Blastn
[2023-06-04 18:00:19,437] [INFO] Running command: blastn -query GCA_001004185.1_ASM100418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/reference_markers.fasta -out GCA_001004185.1_ASM100418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:20,131] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:20,141] [INFO] Selected 1 target genomes.
[2023-06-04 18:00:20,142] [INFO] Target genome list was writen to GCA_001004185.1_ASM100418v1_genomic.fna/target_genomes.txt
[2023-06-04 18:00:20,174] [INFO] Task started: fastANI
[2023-06-04 18:00:20,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgac51a922-8c19-4116-a959-052b36bde757/GCA_001004185.1_ASM100418v1_genomic.fna.gz --refList GCA_001004185.1_ASM100418v1_genomic.fna/target_genomes.txt --output GCA_001004185.1_ASM100418v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:20,576] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:20,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:20,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:20,578] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:20,578] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:00:20,578] [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
--------------------------------------------------------------------------------
[2023-06-04 18:00:20,581] [INFO] DFAST Taxonomy check result was written to GCA_001004185.1_ASM100418v1_genomic.fna/tc_result.tsv
[2023-06-04 18:00:20,581] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:20,581] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:20,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/checkm_data
[2023-06-04 18:00:20,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:20,594] [INFO] Task started: CheckM
[2023-06-04 18:00:20,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001004185.1_ASM100418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001004185.1_ASM100418v1_genomic.fna/checkm_input GCA_001004185.1_ASM100418v1_genomic.fna/checkm_result
[2023-06-04 18:00:34,570] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:34,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:34,592] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:34,592] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:34,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001004185.1_ASM100418v1_genomic.fna/markers.fasta)
[2023-06-04 18:00:34,593] [INFO] Task started: Blastn
[2023-06-04 18:00:34,593] [INFO] Running command: blastn -query GCA_001004185.1_ASM100418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgced3002a-62ba-4374-9942-0c92b6386e72/dqc_reference/reference_markers_gtdb.fasta -out GCA_001004185.1_ASM100418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:35,256] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:35,581] [INFO] Selected 10 target genomes.
[2023-06-04 18:00:35,582] [INFO] Target genome list was writen to GCA_001004185.1_ASM100418v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:35,891] [INFO] Task started: fastANI
[2023-06-04 18:00:35,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgac51a922-8c19-4116-a959-052b36bde757/GCA_001004185.1_ASM100418v1_genomic.fna.gz --refList GCA_001004185.1_ASM100418v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001004185.1_ASM100418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:00:38,764] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:38,767] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:00:38,768] [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_003545515.1	s__UBA10103 sp003545515	98.9818	95	115	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA2100;g__UBA10103	95.0	99.09	99.09	0.80	0.80	2	conclusive
--------------------------------------------------------------------------------
[2023-06-04 18:00:38,769] [INFO] GTDB search result was written to GCA_001004185.1_ASM100418v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:00:38,770] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:00:38,772] [INFO] DFAST_QC result json was written to GCA_001004185.1_ASM100418v1_genomic.fna/dqc_result.json
[2023-06-04 18:00:38,773] [INFO] DFAST_QC completed!
[2023-06-04 18:00:38,773] [INFO] Total running time: 0h0m23s