[2023-06-13 16:10:50,932] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:10:50,938] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:10:50,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference
[2023-06-13 16:10:53,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:10:53,486] [INFO] Task started: Prodigal
[2023-06-13 16:10:53,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg5464de75-160c-469c-a0d0-1b6e1679f1c8/GCA_022563785.1_ASM2256378v1_genomic.fna.gz | prodigal -d GCA_022563785.1_ASM2256378v1_genomic.fna/cds.fna -a GCA_022563785.1_ASM2256378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:10:59,761] [INFO] Task succeeded: Prodigal
[2023-06-13 16:10:59,761] [INFO] Task started: HMMsearch
[2023-06-13 16:10:59,762] [INFO] Running command: hmmsearch --tblout GCA_022563785.1_ASM2256378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/reference_markers.hmm GCA_022563785.1_ASM2256378v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:11:00,023] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:11:00,025] [INFO] Found 6/6 markers.
[2023-06-13 16:11:00,054] [INFO] Query marker FASTA was written to GCA_022563785.1_ASM2256378v1_genomic.fna/markers.fasta
[2023-06-13 16:11:00,055] [INFO] Task started: Blastn
[2023-06-13 16:11:00,055] [INFO] Running command: blastn -query GCA_022563785.1_ASM2256378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/reference_markers.fasta -out GCA_022563785.1_ASM2256378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:11:00,661] [INFO] Task succeeded: Blastn
[2023-06-13 16:11:00,667] [INFO] Selected 20 target genomes.
[2023-06-13 16:11:00,667] [INFO] Target genome list was writen to GCA_022563785.1_ASM2256378v1_genomic.fna/target_genomes.txt
[2023-06-13 16:11:00,672] [INFO] Task started: fastANI
[2023-06-13 16:11:00,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg5464de75-160c-469c-a0d0-1b6e1679f1c8/GCA_022563785.1_ASM2256378v1_genomic.fna.gz --refList GCA_022563785.1_ASM2256378v1_genomic.fna/target_genomes.txt --output GCA_022563785.1_ASM2256378v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:11:16,093] [INFO] Task succeeded: fastANI
[2023-06-13 16:11:16,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:11:16,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:11:16,096] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:11:16,096] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 16:11:16,096] [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
--------------------------------------------------------------------------------
[2023-06-13 16:11:16,099] [INFO] DFAST Taxonomy check result was written to GCA_022563785.1_ASM2256378v1_genomic.fna/tc_result.tsv
[2023-06-13 16:11:16,099] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:11:16,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:11:16,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/checkm_data
[2023-06-13 16:11:16,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:11:16,148] [INFO] Task started: CheckM
[2023-06-13 16:11:16,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563785.1_ASM2256378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563785.1_ASM2256378v1_genomic.fna/checkm_input GCA_022563785.1_ASM2256378v1_genomic.fna/checkm_result
[2023-06-13 16:11:41,398] [INFO] Task succeeded: CheckM
[2023-06-13 16:11:41,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-13 16:11:41,427] [INFO] ===== Completeness check finished =====
[2023-06-13 16:11:41,428] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:11:41,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563785.1_ASM2256378v1_genomic.fna/markers.fasta)
[2023-06-13 16:11:41,429] [INFO] Task started: Blastn
[2023-06-13 16:11:41,429] [INFO] Running command: blastn -query GCA_022563785.1_ASM2256378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29078f7d-0366-495e-9d69-221d1da83bbf/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563785.1_ASM2256378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:11:42,250] [INFO] Task succeeded: Blastn
[2023-06-13 16:11:42,257] [INFO] Selected 13 target genomes.
[2023-06-13 16:11:42,257] [INFO] Target genome list was writen to GCA_022563785.1_ASM2256378v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:11:42,271] [INFO] Task started: fastANI
[2023-06-13 16:11:42,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg5464de75-160c-469c-a0d0-1b6e1679f1c8/GCA_022563785.1_ASM2256378v1_genomic.fna.gz --refList GCA_022563785.1_ASM2256378v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563785.1_ASM2256378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:11:48,450] [INFO] Task succeeded: fastANI
[2023-06-13 16:11:48,464] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:11:48,465] [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_001643535.1	s__CSP1-5 sp001643535	98.8411	321	725	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__CSP1-5;g__CSP1-5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012974305.1	s__CSP1-5 sp012974305	80.0925	361	725	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__CSP1-5;g__CSP1-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001443495.1	s__CSP1-5 sp001443495	79.332	346	725	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__CSP1-5;g__CSP1-5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:11:48,468] [INFO] GTDB search result was written to GCA_022563785.1_ASM2256378v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:11:48,469] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:11:48,477] [INFO] DFAST_QC result json was written to GCA_022563785.1_ASM2256378v1_genomic.fna/dqc_result.json
[2023-06-13 16:11:48,478] [INFO] DFAST_QC completed!
[2023-06-13 16:11:48,478] [INFO] Total running time: 0h0m58s