[2023-06-17 09:46:41,383] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:46:41,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:46:41,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/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 09:46:43,335] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc4a297a-62df-4040-956a-feb424998ee1/GCA_009920095.1_ASM992009v1_genomic.fna.gz | prodigal -d GCA_009920095.1_ASM992009v1_genomic.fna/cds.fna -a GCA_009920095.1_ASM992009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:47:06,234] [INFO] Task succeeded: Prodigal
[2023-06-17 09:47:06,235] [INFO] Task started: HMMsearch
[2023-06-17 09:47:06,235] [INFO] Running command: hmmsearch --tblout GCA_009920095.1_ASM992009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/reference_markers.hmm GCA_009920095.1_ASM992009v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:47:06,482] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:47:06,483] [INFO] Found 6/6 markers.
[2023-06-17 09:47:06,518] [INFO] Query marker FASTA was written to GCA_009920095.1_ASM992009v1_genomic.fna/markers.fasta
[2023-06-17 09:47:06,518] [INFO] Task started: Blastn
[2023-06-17 09:47:06,519] [INFO] Running command: blastn -query GCA_009920095.1_ASM992009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/reference_markers.fasta -out GCA_009920095.1_ASM992009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:47:07,139] [INFO] Task succeeded: Blastn
[2023-06-17 09:47:07,144] [INFO] Selected 10 target genomes.
[2023-06-17 09:47:07,144] [INFO] Target genome list was writen to GCA_009920095.1_ASM992009v1_genomic.fna/target_genomes.txt
[2023-06-17 09:47:07,146] [INFO] Task started: fastANI
[2023-06-17 09:47:07,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc4a297a-62df-4040-956a-feb424998ee1/GCA_009920095.1_ASM992009v1_genomic.fna.gz --refList GCA_009920095.1_ASM992009v1_genomic.fna/target_genomes.txt --output GCA_009920095.1_ASM992009v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:47:14,071] [INFO] Task succeeded: fastANI
[2023-06-17 09:47:14,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:47:14,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:47:14,075] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:47:14,075] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:47:14,075] [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 09:47:14,077] [INFO] DFAST Taxonomy check result was written to GCA_009920095.1_ASM992009v1_genomic.fna/tc_result.tsv
[2023-06-17 09:47:14,078] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:47:14,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:47:14,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/checkm_data
[2023-06-17 09:47:14,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:47:14,124] [INFO] Task started: CheckM
[2023-06-17 09:47:14,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009920095.1_ASM992009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009920095.1_ASM992009v1_genomic.fna/checkm_input GCA_009920095.1_ASM992009v1_genomic.fna/checkm_result
[2023-06-17 09:48:22,298] [INFO] Task succeeded: CheckM
[2023-06-17 09:48:22,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.75%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:48:22,322] [INFO] ===== Completeness check finished =====
[2023-06-17 09:48:22,322] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:48:22,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009920095.1_ASM992009v1_genomic.fna/markers.fasta)
[2023-06-17 09:48:22,323] [INFO] Task started: Blastn
[2023-06-17 09:48:22,323] [INFO] Running command: blastn -query GCA_009920095.1_ASM992009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a9186a2-897b-4c2a-ac66-7394854615d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_009920095.1_ASM992009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:48:23,329] [INFO] Task succeeded: Blastn
[2023-06-17 09:48:23,334] [INFO] Selected 30 target genomes.
[2023-06-17 09:48:23,334] [INFO] Target genome list was writen to GCA_009920095.1_ASM992009v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:48:23,349] [INFO] Task started: fastANI
[2023-06-17 09:48:23,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc4a297a-62df-4040-956a-feb424998ee1/GCA_009920095.1_ASM992009v1_genomic.fna.gz --refList GCA_009920095.1_ASM992009v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009920095.1_ASM992009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:48:45,970] [INFO] Task succeeded: fastANI
[2023-06-17 09:48:45,975] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:48:45,975] [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_002686885.1	s__UBA7971 sp002686885	78.8521	195	982	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AAA164-E04;g__UBA7971	95.0	98.29	95.01	0.90	0.82	6	-
--------------------------------------------------------------------------------
[2023-06-17 09:48:45,978] [INFO] GTDB search result was written to GCA_009920095.1_ASM992009v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:48:45,978] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:48:45,981] [INFO] DFAST_QC result json was written to GCA_009920095.1_ASM992009v1_genomic.fna/dqc_result.json
[2023-06-17 09:48:45,981] [INFO] DFAST_QC completed!
[2023-06-17 09:48:45,982] [INFO] Total running time: 0h2m5s