[2023-06-13 12:35:08,337] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:35:08,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:35:08,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference
[2023-06-13 12:35:10,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:35:10,502] [INFO] Task started: Prodigal
[2023-06-13 12:35:10,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed313c0-f748-42d1-b41f-761536cacd02/GCA_022867025.1_ASM2286702v1_genomic.fna.gz | prodigal -d GCA_022867025.1_ASM2286702v1_genomic.fna/cds.fna -a GCA_022867025.1_ASM2286702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:35:15,190] [INFO] Task succeeded: Prodigal
[2023-06-13 12:35:15,190] [INFO] Task started: HMMsearch
[2023-06-13 12:35:15,191] [INFO] Running command: hmmsearch --tblout GCA_022867025.1_ASM2286702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/reference_markers.hmm GCA_022867025.1_ASM2286702v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:35:15,382] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:35:15,384] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ed313c0-f748-42d1-b41f-761536cacd02/GCA_022867025.1_ASM2286702v1_genomic.fna.gz]
[2023-06-13 12:35:15,410] [INFO] Query marker FASTA was written to GCA_022867025.1_ASM2286702v1_genomic.fna/markers.fasta
[2023-06-13 12:35:15,410] [INFO] Task started: Blastn
[2023-06-13 12:35:15,410] [INFO] Running command: blastn -query GCA_022867025.1_ASM2286702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/reference_markers.fasta -out GCA_022867025.1_ASM2286702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:35:16,104] [INFO] Task succeeded: Blastn
[2023-06-13 12:35:16,112] [INFO] Selected 25 target genomes.
[2023-06-13 12:35:16,112] [INFO] Target genome list was writen to GCA_022867025.1_ASM2286702v1_genomic.fna/target_genomes.txt
[2023-06-13 12:35:16,118] [INFO] Task started: fastANI
[2023-06-13 12:35:16,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed313c0-f748-42d1-b41f-761536cacd02/GCA_022867025.1_ASM2286702v1_genomic.fna.gz --refList GCA_022867025.1_ASM2286702v1_genomic.fna/target_genomes.txt --output GCA_022867025.1_ASM2286702v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:35:36,797] [INFO] Task succeeded: fastANI
[2023-06-13 12:35:36,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:35:36,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:35:36,801] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:35:36,801] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 12:35:36,801] [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 12:35:36,804] [INFO] DFAST Taxonomy check result was written to GCA_022867025.1_ASM2286702v1_genomic.fna/tc_result.tsv
[2023-06-13 12:35:36,805] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:35:36,805] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:35:36,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/checkm_data
[2023-06-13 12:35:36,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:35:36,836] [INFO] Task started: CheckM
[2023-06-13 12:35:36,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022867025.1_ASM2286702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022867025.1_ASM2286702v1_genomic.fna/checkm_input GCA_022867025.1_ASM2286702v1_genomic.fna/checkm_result
[2023-06-13 12:35:57,566] [INFO] Task succeeded: CheckM
[2023-06-13 12:35:57,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.01%
Contamintation: 13.31%
Strain heterogeneity: 44.44%
--------------------------------------------------------------------------------
[2023-06-13 12:35:57,609] [INFO] ===== Completeness check finished =====
[2023-06-13 12:35:57,609] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:35:57,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022867025.1_ASM2286702v1_genomic.fna/markers.fasta)
[2023-06-13 12:35:57,610] [INFO] Task started: Blastn
[2023-06-13 12:35:57,610] [INFO] Running command: blastn -query GCA_022867025.1_ASM2286702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9640479e-43ff-4c98-b393-30d23dd66f9f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022867025.1_ASM2286702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:35:58,585] [INFO] Task succeeded: Blastn
[2023-06-13 12:35:58,592] [INFO] Selected 16 target genomes.
[2023-06-13 12:35:58,592] [INFO] Target genome list was writen to GCA_022867025.1_ASM2286702v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:35:58,624] [INFO] Task started: fastANI
[2023-06-13 12:35:58,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed313c0-f748-42d1-b41f-761536cacd02/GCA_022867025.1_ASM2286702v1_genomic.fna.gz --refList GCA_022867025.1_ASM2286702v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022867025.1_ASM2286702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:36:06,352] [INFO] Task succeeded: fastANI
[2023-06-13 12:36:06,360] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 12:36:06,361] [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_018821365.1	s__JAHJML01 sp018821365	81.9111	204	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__JAHJML01	95.0	99.66	99.66	0.91	0.91	2	-
GCA_016870535.1	s__VGBK01 sp016870535	77.6875	64	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__VGBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932695.1	s__VGBK01 sp016932695	77.6182	66	262	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA11373;g__VGBK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:36:06,364] [INFO] GTDB search result was written to GCA_022867025.1_ASM2286702v1_genomic.fna/result_gtdb.tsv
[2023-06-13 12:36:06,365] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:36:06,368] [INFO] DFAST_QC result json was written to GCA_022867025.1_ASM2286702v1_genomic.fna/dqc_result.json
[2023-06-13 12:36:06,369] [INFO] DFAST_QC completed!
[2023-06-13 12:36:06,369] [INFO] Total running time: 0h0m58s