[2023-06-05 18:01:55,958] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:01:55,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:01:55,960] [INFO] DQC Reference Directory: /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference
[2023-06-05 18:01:57,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:01:57,302] [INFO] Task started: Prodigal
[2023-06-05 18:01:57,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgec293070-bf2c-4319-a387-54ebb52d2921/GCA_001783775.1_ASM178377v1_genomic.fna.gz | prodigal -d GCA_001783775.1_ASM178377v1_genomic.fna/cds.fna -a GCA_001783775.1_ASM178377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:01,384] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:01,385] [INFO] Task started: HMMsearch
[2023-06-05 18:02:01,385] [INFO] Running command: hmmsearch --tblout GCA_001783775.1_ASM178377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/reference_markers.hmm GCA_001783775.1_ASM178377v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:01,696] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:01,697] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgec293070-bf2c-4319-a387-54ebb52d2921/GCA_001783775.1_ASM178377v1_genomic.fna.gz]
[2023-06-05 18:02:01,719] [INFO] Query marker FASTA was written to GCA_001783775.1_ASM178377v1_genomic.fna/markers.fasta
[2023-06-05 18:02:01,720] [INFO] Task started: Blastn
[2023-06-05 18:02:01,720] [INFO] Running command: blastn -query GCA_001783775.1_ASM178377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/reference_markers.fasta -out GCA_001783775.1_ASM178377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:02,299] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:02,311] [INFO] Selected 3 target genomes.
[2023-06-05 18:02:02,312] [INFO] Target genome list was writen to GCA_001783775.1_ASM178377v1_genomic.fna/target_genomes.txt
[2023-06-05 18:02:02,315] [INFO] Task started: fastANI
[2023-06-05 18:02:02,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgec293070-bf2c-4319-a387-54ebb52d2921/GCA_001783775.1_ASM178377v1_genomic.fna.gz --refList GCA_001783775.1_ASM178377v1_genomic.fna/target_genomes.txt --output GCA_001783775.1_ASM178377v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:03,781] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:03,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:03,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:03,790] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:03,791] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:02:03,791] [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
--------------------------------------------------------------------------------
[2023-06-05 18:02:03,793] [INFO] DFAST Taxonomy check result was written to GCA_001783775.1_ASM178377v1_genomic.fna/tc_result.tsv
[2023-06-05 18:02:03,794] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:03,794] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:03,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/checkm_data
[2023-06-05 18:02:03,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:03,848] [INFO] Task started: CheckM
[2023-06-05 18:02:03,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001783775.1_ASM178377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001783775.1_ASM178377v1_genomic.fna/checkm_input GCA_001783775.1_ASM178377v1_genomic.fna/checkm_result
[2023-06-05 18:02:23,562] [INFO] Task succeeded: CheckM
[2023-06-05 18:02:23,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:02:23,584] [INFO] ===== Completeness check finished =====
[2023-06-05 18:02:23,584] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:02:23,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001783775.1_ASM178377v1_genomic.fna/markers.fasta)
[2023-06-05 18:02:23,585] [INFO] Task started: Blastn
[2023-06-05 18:02:23,585] [INFO] Running command: blastn -query GCA_001783775.1_ASM178377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2bf865c-0d56-4ba2-9775-7470b5434c26/dqc_reference/reference_markers_gtdb.fasta -out GCA_001783775.1_ASM178377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:24,045] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:24,050] [INFO] Selected 13 target genomes.
[2023-06-05 18:02:24,050] [INFO] Target genome list was writen to GCA_001783775.1_ASM178377v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:02:24,057] [INFO] Task started: fastANI
[2023-06-05 18:02:24,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgec293070-bf2c-4319-a387-54ebb52d2921/GCA_001783775.1_ASM178377v1_genomic.fna.gz --refList GCA_001783775.1_ASM178377v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001783775.1_ASM178377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:02:26,851] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:26,855] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:02:26,855] [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_001784115.1	s__2-01-FULL-37-20 sp001784115	99.9401	274	306	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__Levybacterales;f__UBA12049;g__2-01-FULL-37-20	95.0	99.96	99.94	0.91	0.90	5	conclusive
--------------------------------------------------------------------------------
[2023-06-05 18:02:26,858] [INFO] GTDB search result was written to GCA_001783775.1_ASM178377v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:02:26,859] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:02:26,862] [INFO] DFAST_QC result json was written to GCA_001783775.1_ASM178377v1_genomic.fna/dqc_result.json
[2023-06-05 18:02:26,862] [INFO] DFAST_QC completed!
[2023-06-05 18:02:26,862] [INFO] Total running time: 0h0m31s