[2023-06-05 18:44:28,301] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:44:28,303] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:44:28,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference
[2023-06-05 18:44:29,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:44:29,478] [INFO] Task started: Prodigal
[2023-06-05 18:44:29,478] [INFO] Running command: gunzip -c /var/lib/cwl/stgddce14c2-5879-43a9-9697-dfd75ba3c378/GCA_010026895.1_ASM1002689v1_genomic.fna.gz | prodigal -d GCA_010026895.1_ASM1002689v1_genomic.fna/cds.fna -a GCA_010026895.1_ASM1002689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:44:31,195] [INFO] Task succeeded: Prodigal
[2023-06-05 18:44:31,196] [INFO] Task started: HMMsearch
[2023-06-05 18:44:31,196] [INFO] Running command: hmmsearch --tblout GCA_010026895.1_ASM1002689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/reference_markers.hmm GCA_010026895.1_ASM1002689v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:44:31,337] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:44:31,338] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgddce14c2-5879-43a9-9697-dfd75ba3c378/GCA_010026895.1_ASM1002689v1_genomic.fna.gz]
[2023-06-05 18:44:31,366] [INFO] Query marker FASTA was written to GCA_010026895.1_ASM1002689v1_genomic.fna/markers.fasta
[2023-06-05 18:44:31,366] [INFO] Task started: Blastn
[2023-06-05 18:44:31,367] [INFO] Running command: blastn -query GCA_010026895.1_ASM1002689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/reference_markers.fasta -out GCA_010026895.1_ASM1002689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:44:31,977] [INFO] Task succeeded: Blastn
[2023-06-05 18:44:31,980] [INFO] Selected 14 target genomes.
[2023-06-05 18:44:31,981] [INFO] Target genome list was writen to GCA_010026895.1_ASM1002689v1_genomic.fna/target_genomes.txt
[2023-06-05 18:44:31,986] [INFO] Task started: fastANI
[2023-06-05 18:44:31,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgddce14c2-5879-43a9-9697-dfd75ba3c378/GCA_010026895.1_ASM1002689v1_genomic.fna.gz --refList GCA_010026895.1_ASM1002689v1_genomic.fna/target_genomes.txt --output GCA_010026895.1_ASM1002689v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:44:38,888] [INFO] Task succeeded: fastANI
[2023-06-05 18:44:38,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:44:38,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:44:38,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:44:38,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:44:38,890] [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
--------------------------------------------------------------------------------
[2023-06-05 18:44:38,892] [INFO] DFAST Taxonomy check result was written to GCA_010026895.1_ASM1002689v1_genomic.fna/tc_result.tsv
[2023-06-05 18:44:38,892] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:44:38,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:44:38,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/checkm_data
[2023-06-05 18:44:38,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:44:38,921] [INFO] Task started: CheckM
[2023-06-05 18:44:38,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010026895.1_ASM1002689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010026895.1_ASM1002689v1_genomic.fna/checkm_input GCA_010026895.1_ASM1002689v1_genomic.fna/checkm_result
[2023-06-05 18:44:52,637] [INFO] Task succeeded: CheckM
[2023-06-05 18:44:52,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.36%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:44:52,654] [INFO] ===== Completeness check finished =====
[2023-06-05 18:44:52,654] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:44:52,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010026895.1_ASM1002689v1_genomic.fna/markers.fasta)
[2023-06-05 18:44:52,655] [INFO] Task started: Blastn
[2023-06-05 18:44:52,655] [INFO] Running command: blastn -query GCA_010026895.1_ASM1002689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78e44b26-4164-40e1-8b4a-b91972e577d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_010026895.1_ASM1002689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:44:53,281] [INFO] Task succeeded: Blastn
[2023-06-05 18:44:53,284] [INFO] Selected 11 target genomes.
[2023-06-05 18:44:53,284] [INFO] Target genome list was writen to GCA_010026895.1_ASM1002689v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:44:53,298] [INFO] Task started: fastANI
[2023-06-05 18:44:53,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgddce14c2-5879-43a9-9697-dfd75ba3c378/GCA_010026895.1_ASM1002689v1_genomic.fna.gz --refList GCA_010026895.1_ASM1002689v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010026895.1_ASM1002689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:44:55,628] [INFO] Task succeeded: fastANI
[2023-06-05 18:44:55,632] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:44:55,632] [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_009927245.1	s__Rhodoluna sp009927245	96.8593	94	126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.72	98.72	0.75	0.75	2	conclusive
GCA_016462375.1	s__Rhodoluna sp016462375	81.6447	72	126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832875.1	s__Rhodoluna sp903832875	80.3918	61	126	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.70	97.77	0.86	0.82	7	-
--------------------------------------------------------------------------------
[2023-06-05 18:44:55,634] [INFO] GTDB search result was written to GCA_010026895.1_ASM1002689v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:44:55,634] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:44:55,636] [INFO] DFAST_QC result json was written to GCA_010026895.1_ASM1002689v1_genomic.fna/dqc_result.json
[2023-06-05 18:44:55,636] [INFO] DFAST_QC completed!
[2023-06-05 18:44:55,636] [INFO] Total running time: 0h0m27s