[2023-06-28 03:36:05,455] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:36:05,458] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:36:05,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference
[2023-06-28 03:36:06,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:36:06,806] [INFO] Task started: Prodigal
[2023-06-28 03:36:06,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg999915d0-dd11-49f2-bb0f-c4836a5e1a6b/GCA_017883765.1_ASM1788376v1_genomic.fna.gz | prodigal -d GCA_017883765.1_ASM1788376v1_genomic.fna/cds.fna -a GCA_017883765.1_ASM1788376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:36:07,482] [INFO] Task succeeded: Prodigal
[2023-06-28 03:36:07,483] [INFO] Task started: HMMsearch
[2023-06-28 03:36:07,483] [INFO] Running command: hmmsearch --tblout GCA_017883765.1_ASM1788376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/reference_markers.hmm GCA_017883765.1_ASM1788376v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:36:07,701] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:36:07,703] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg999915d0-dd11-49f2-bb0f-c4836a5e1a6b/GCA_017883765.1_ASM1788376v1_genomic.fna.gz]
[2023-06-28 03:36:07,713] [INFO] Query marker FASTA was written to GCA_017883765.1_ASM1788376v1_genomic.fna/markers.fasta
[2023-06-28 03:36:07,713] [INFO] Task started: Blastn
[2023-06-28 03:36:07,713] [INFO] Running command: blastn -query GCA_017883765.1_ASM1788376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/reference_markers.fasta -out GCA_017883765.1_ASM1788376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:36:08,434] [INFO] Task succeeded: Blastn
[2023-06-28 03:36:08,440] [INFO] Selected 20 target genomes.
[2023-06-28 03:36:08,441] [INFO] Target genome list was writen to GCA_017883765.1_ASM1788376v1_genomic.fna/target_genomes.txt
[2023-06-28 03:36:08,449] [INFO] Task started: fastANI
[2023-06-28 03:36:08,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg999915d0-dd11-49f2-bb0f-c4836a5e1a6b/GCA_017883765.1_ASM1788376v1_genomic.fna.gz --refList GCA_017883765.1_ASM1788376v1_genomic.fna/target_genomes.txt --output GCA_017883765.1_ASM1788376v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:36:21,684] [INFO] Task succeeded: fastANI
[2023-06-28 03:36:21,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:36:21,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:36:21,687] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:36:21,687] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:36:21,687] [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
--------------------------------------------------------------------------------
[2023-06-28 03:36:21,689] [INFO] DFAST Taxonomy check result was written to GCA_017883765.1_ASM1788376v1_genomic.fna/tc_result.tsv
[2023-06-28 03:36:21,690] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:36:21,690] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:36:21,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/checkm_data
[2023-06-28 03:36:21,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:36:21,706] [INFO] Task started: CheckM
[2023-06-28 03:36:21,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017883765.1_ASM1788376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017883765.1_ASM1788376v1_genomic.fna/checkm_input GCA_017883765.1_ASM1788376v1_genomic.fna/checkm_result
[2023-06-28 03:36:33,095] [INFO] Task succeeded: CheckM
[2023-06-28 03:36:33,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:36:33,125] [INFO] ===== Completeness check finished =====
[2023-06-28 03:36:33,126] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:36:33,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017883765.1_ASM1788376v1_genomic.fna/markers.fasta)
[2023-06-28 03:36:33,126] [INFO] Task started: Blastn
[2023-06-28 03:36:33,126] [INFO] Running command: blastn -query GCA_017883765.1_ASM1788376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3660797a-2609-412d-b6b6-4cd2ee8da819/dqc_reference/reference_markers_gtdb.fasta -out GCA_017883765.1_ASM1788376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:36:33,866] [INFO] Task succeeded: Blastn
[2023-06-28 03:36:33,871] [INFO] Selected 16 target genomes.
[2023-06-28 03:36:33,871] [INFO] Target genome list was writen to GCA_017883765.1_ASM1788376v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:36:33,904] [INFO] Task started: fastANI
[2023-06-28 03:36:33,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg999915d0-dd11-49f2-bb0f-c4836a5e1a6b/GCA_017883765.1_ASM1788376v1_genomic.fna.gz --refList GCA_017883765.1_ASM1788376v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017883765.1_ASM1788376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:36:39,988] [INFO] Task succeeded: fastANI
[2023-06-28 03:36:39,991] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:36:39,991] [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
GCF_000441555.1	s__Profftella armatura	99.8104	144	145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__Profftella	95.0	99.98	99.98	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2023-06-28 03:36:39,993] [INFO] GTDB search result was written to GCA_017883765.1_ASM1788376v1_genomic.fna/result_gtdb.tsv
[2023-06-28 03:36:39,994] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:36:39,996] [INFO] DFAST_QC result json was written to GCA_017883765.1_ASM1788376v1_genomic.fna/dqc_result.json
[2023-06-28 03:36:39,996] [INFO] DFAST_QC completed!
[2023-06-28 03:36:39,996] [INFO] Total running time: 0h0m35s