[2023-06-27 22:54:04,545] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:54:04,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:54:04,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference
[2023-06-27 22:54:06,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:54:06,871] [INFO] Task started: Prodigal
[2023-06-27 22:54:06,872] [INFO] Running command: gunzip -c /var/lib/cwl/stgcead79a0-6b45-4b5c-8041-18679e221cfa/GCA_002389445.1_ASM238944v1_genomic.fna.gz | prodigal -d GCA_002389445.1_ASM238944v1_genomic.fna/cds.fna -a GCA_002389445.1_ASM238944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:54:18,264] [INFO] Task succeeded: Prodigal
[2023-06-27 22:54:18,264] [INFO] Task started: HMMsearch
[2023-06-27 22:54:18,264] [INFO] Running command: hmmsearch --tblout GCA_002389445.1_ASM238944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/reference_markers.hmm GCA_002389445.1_ASM238944v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:54:18,460] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:54:18,461] [INFO] Found 6/6 markers.
[2023-06-27 22:54:18,494] [INFO] Query marker FASTA was written to GCA_002389445.1_ASM238944v1_genomic.fna/markers.fasta
[2023-06-27 22:54:18,494] [INFO] Task started: Blastn
[2023-06-27 22:54:18,494] [INFO] Running command: blastn -query GCA_002389445.1_ASM238944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/reference_markers.fasta -out GCA_002389445.1_ASM238944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:19,054] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:19,058] [INFO] Selected 22 target genomes.
[2023-06-27 22:54:19,058] [INFO] Target genome list was writen to GCA_002389445.1_ASM238944v1_genomic.fna/target_genomes.txt
[2023-06-27 22:54:19,063] [INFO] Task started: fastANI
[2023-06-27 22:54:19,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgcead79a0-6b45-4b5c-8041-18679e221cfa/GCA_002389445.1_ASM238944v1_genomic.fna.gz --refList GCA_002389445.1_ASM238944v1_genomic.fna/target_genomes.txt --output GCA_002389445.1_ASM238944v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:54:38,198] [INFO] Task succeeded: fastANI
[2023-06-27 22:54:38,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:54:38,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:54:38,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:54:38,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 22:54:38,200] [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
--------------------------------------------------------------------------------
[2023-06-27 22:54:38,202] [INFO] DFAST Taxonomy check result was written to GCA_002389445.1_ASM238944v1_genomic.fna/tc_result.tsv
[2023-06-27 22:54:38,205] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:54:38,205] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:54:38,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/checkm_data
[2023-06-27 22:54:38,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:54:38,245] [INFO] Task started: CheckM
[2023-06-27 22:54:38,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002389445.1_ASM238944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002389445.1_ASM238944v1_genomic.fna/checkm_input GCA_002389445.1_ASM238944v1_genomic.fna/checkm_result
[2023-06-27 22:55:14,017] [INFO] Task succeeded: CheckM
[2023-06-27 22:55:14,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:55:14,037] [INFO] ===== Completeness check finished =====
[2023-06-27 22:55:14,038] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:55:14,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002389445.1_ASM238944v1_genomic.fna/markers.fasta)
[2023-06-27 22:55:14,038] [INFO] Task started: Blastn
[2023-06-27 22:55:14,038] [INFO] Running command: blastn -query GCA_002389445.1_ASM238944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1db0cf93-48e4-4917-8047-72a5bb866c27/dqc_reference/reference_markers_gtdb.fasta -out GCA_002389445.1_ASM238944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:55:14,799] [INFO] Task succeeded: Blastn
[2023-06-27 22:55:14,803] [INFO] Selected 20 target genomes.
[2023-06-27 22:55:14,803] [INFO] Target genome list was writen to GCA_002389445.1_ASM238944v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:55:14,816] [INFO] Task started: fastANI
[2023-06-27 22:55:14,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgcead79a0-6b45-4b5c-8041-18679e221cfa/GCA_002389445.1_ASM238944v1_genomic.fna.gz --refList GCA_002389445.1_ASM238944v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002389445.1_ASM238944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:55:28,737] [INFO] Task succeeded: fastANI
[2023-06-27 22:55:28,740] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:55:28,740] [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_002352645.1	s__UBA2766 sp002352645	99.8483	1111	1183	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA2766;f__UBA2766;g__UBA2766	95.0	99.85	99.85	0.94	0.94	2	conclusive
--------------------------------------------------------------------------------
[2023-06-27 22:55:28,742] [INFO] GTDB search result was written to GCA_002389445.1_ASM238944v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:55:28,743] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:55:28,745] [INFO] DFAST_QC result json was written to GCA_002389445.1_ASM238944v1_genomic.fna/dqc_result.json
[2023-06-27 22:55:28,745] [INFO] DFAST_QC completed!
[2023-06-27 22:55:28,745] [INFO] Total running time: 0h1m24s