[2023-06-19 14:48:49,448] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:48:49,451] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:48:49,452] [INFO] DQC Reference Directory: /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference
[2023-06-19 14:48:50,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:48:50,574] [INFO] Task started: Prodigal
[2023-06-19 14:48:50,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg05d15bb3-e792-409a-bcaf-69efef68f7a1/GCA_018882785.1_ASM1888278v1_genomic.fna.gz | prodigal -d GCA_018882785.1_ASM1888278v1_genomic.fna/cds.fna -a GCA_018882785.1_ASM1888278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:48:56,007] [INFO] Task succeeded: Prodigal
[2023-06-19 14:48:56,008] [INFO] Task started: HMMsearch
[2023-06-19 14:48:56,008] [INFO] Running command: hmmsearch --tblout GCA_018882785.1_ASM1888278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/reference_markers.hmm GCA_018882785.1_ASM1888278v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:48:56,191] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:48:56,192] [INFO] Found 6/6 markers.
[2023-06-19 14:48:56,211] [INFO] Query marker FASTA was written to GCA_018882785.1_ASM1888278v1_genomic.fna/markers.fasta
[2023-06-19 14:48:56,211] [INFO] Task started: Blastn
[2023-06-19 14:48:56,211] [INFO] Running command: blastn -query GCA_018882785.1_ASM1888278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/reference_markers.fasta -out GCA_018882785.1_ASM1888278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:48:56,776] [INFO] Task succeeded: Blastn
[2023-06-19 14:48:56,781] [INFO] Selected 30 target genomes.
[2023-06-19 14:48:56,781] [INFO] Target genome list was writen to GCA_018882785.1_ASM1888278v1_genomic.fna/target_genomes.txt
[2023-06-19 14:48:56,785] [INFO] Task started: fastANI
[2023-06-19 14:48:56,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d15bb3-e792-409a-bcaf-69efef68f7a1/GCA_018882785.1_ASM1888278v1_genomic.fna.gz --refList GCA_018882785.1_ASM1888278v1_genomic.fna/target_genomes.txt --output GCA_018882785.1_ASM1888278v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:49:19,751] [INFO] Task succeeded: fastANI
[2023-06-19 14:49:19,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:49:19,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:49:19,753] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:49:19,753] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:49:19,753] [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
--------------------------------------------------------------------------------
[2023-06-19 14:49:19,754] [INFO] DFAST Taxonomy check result was written to GCA_018882785.1_ASM1888278v1_genomic.fna/tc_result.tsv
[2023-06-19 14:49:19,755] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:49:19,755] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:49:19,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/checkm_data
[2023-06-19 14:49:19,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:49:19,782] [INFO] Task started: CheckM
[2023-06-19 14:49:19,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018882785.1_ASM1888278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018882785.1_ASM1888278v1_genomic.fna/checkm_input GCA_018882785.1_ASM1888278v1_genomic.fna/checkm_result
[2023-06-19 14:49:40,585] [INFO] Task succeeded: CheckM
[2023-06-19 14:49:40,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 14:49:40,605] [INFO] ===== Completeness check finished =====
[2023-06-19 14:49:40,605] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:49:40,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018882785.1_ASM1888278v1_genomic.fna/markers.fasta)
[2023-06-19 14:49:40,605] [INFO] Task started: Blastn
[2023-06-19 14:49:40,605] [INFO] Running command: blastn -query GCA_018882785.1_ASM1888278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge363ca31-35a5-42fe-8f96-aa50e0c5e611/dqc_reference/reference_markers_gtdb.fasta -out GCA_018882785.1_ASM1888278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:49:41,388] [INFO] Task succeeded: Blastn
[2023-06-19 14:49:41,391] [INFO] Selected 18 target genomes.
[2023-06-19 14:49:41,391] [INFO] Target genome list was writen to GCA_018882785.1_ASM1888278v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:49:41,423] [INFO] Task started: fastANI
[2023-06-19 14:49:41,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d15bb3-e792-409a-bcaf-69efef68f7a1/GCA_018882785.1_ASM1888278v1_genomic.fna.gz --refList GCA_018882785.1_ASM1888278v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018882785.1_ASM1888278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:49:51,843] [INFO] Task succeeded: fastANI
[2023-06-19 14:49:51,849] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:49:51,849] [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_018882785.1	s__UBA954 sp018882785	100.0	680	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018970545.1	s__UBA954 sp018970545	78.4316	213	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924525.1	s__UBA954 sp009924525	78.3866	181	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882795.1	s__UBA954 sp018882795	77.9912	242	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969705.1	s__UBA954 sp018969705	77.6699	149	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002293155.1	s__UBA954 sp002293155	76.9714	80	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	98.25	97.64	0.86	0.78	18	-
GCA_009646425.1	s__UBA2463 sp009646425	76.9514	75	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	95.85	95.85	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:49:51,850] [INFO] GTDB search result was written to GCA_018882785.1_ASM1888278v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:49:51,851] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:49:51,853] [INFO] DFAST_QC result json was written to GCA_018882785.1_ASM1888278v1_genomic.fna/dqc_result.json
[2023-06-19 14:49:51,853] [INFO] DFAST_QC completed!
[2023-06-19 14:49:51,853] [INFO] Total running time: 0h1m2s