[2023-06-30 20:54:51,794] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:54:51,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:54:51,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference
[2023-06-30 20:54:53,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:54:53,215] [INFO] Task started: Prodigal
[2023-06-30 20:54:53,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg750d673f-8ba1-4f4f-90c9-c359a9469406/GCA_024408295.1_ASM2440829v1_genomic.fna.gz | prodigal -d GCA_024408295.1_ASM2440829v1_genomic.fna/cds.fna -a GCA_024408295.1_ASM2440829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:54:55,672] [INFO] Task succeeded: Prodigal
[2023-06-30 20:54:55,673] [INFO] Task started: HMMsearch
[2023-06-30 20:54:55,673] [INFO] Running command: hmmsearch --tblout GCA_024408295.1_ASM2440829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/reference_markers.hmm GCA_024408295.1_ASM2440829v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:54:55,924] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:54:55,925] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg750d673f-8ba1-4f4f-90c9-c359a9469406/GCA_024408295.1_ASM2440829v1_genomic.fna.gz]
[2023-06-30 20:54:55,946] [INFO] Query marker FASTA was written to GCA_024408295.1_ASM2440829v1_genomic.fna/markers.fasta
[2023-06-30 20:54:55,947] [INFO] Task started: Blastn
[2023-06-30 20:54:55,947] [INFO] Running command: blastn -query GCA_024408295.1_ASM2440829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/reference_markers.fasta -out GCA_024408295.1_ASM2440829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:54:56,522] [INFO] Task succeeded: Blastn
[2023-06-30 20:54:56,526] [INFO] Selected 11 target genomes.
[2023-06-30 20:54:56,526] [INFO] Target genome list was writen to GCA_024408295.1_ASM2440829v1_genomic.fna/target_genomes.txt
[2023-06-30 20:54:56,530] [INFO] Task started: fastANI
[2023-06-30 20:54:56,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg750d673f-8ba1-4f4f-90c9-c359a9469406/GCA_024408295.1_ASM2440829v1_genomic.fna.gz --refList GCA_024408295.1_ASM2440829v1_genomic.fna/target_genomes.txt --output GCA_024408295.1_ASM2440829v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:01,490] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:01,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:01,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:01,495] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:55:01,495] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:55:01,495] [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
--------------------------------------------------------------------------------
[2023-06-30 20:55:01,498] [INFO] DFAST Taxonomy check result was written to GCA_024408295.1_ASM2440829v1_genomic.fna/tc_result.tsv
[2023-06-30 20:55:01,499] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:01,499] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:01,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/checkm_data
[2023-06-30 20:55:01,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:01,522] [INFO] Task started: CheckM
[2023-06-30 20:55:01,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024408295.1_ASM2440829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024408295.1_ASM2440829v1_genomic.fna/checkm_input GCA_024408295.1_ASM2440829v1_genomic.fna/checkm_result
[2023-06-30 20:55:17,976] [INFO] Task succeeded: CheckM
[2023-06-30 20:55:17,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:55:17,996] [INFO] ===== Completeness check finished =====
[2023-06-30 20:55:17,997] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:55:17,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024408295.1_ASM2440829v1_genomic.fna/markers.fasta)
[2023-06-30 20:55:17,997] [INFO] Task started: Blastn
[2023-06-30 20:55:17,997] [INFO] Running command: blastn -query GCA_024408295.1_ASM2440829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c1622d3-9a50-4b55-80df-e6a89f982730/dqc_reference/reference_markers_gtdb.fasta -out GCA_024408295.1_ASM2440829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:18,702] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:18,707] [INFO] Selected 12 target genomes.
[2023-06-30 20:55:18,707] [INFO] Target genome list was writen to GCA_024408295.1_ASM2440829v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:55:18,739] [INFO] Task started: fastANI
[2023-06-30 20:55:18,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg750d673f-8ba1-4f4f-90c9-c359a9469406/GCA_024408295.1_ASM2440829v1_genomic.fna.gz --refList GCA_024408295.1_ASM2440829v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024408295.1_ASM2440829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:55:21,741] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:21,744] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:55:21,745] [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_002314915.1	s__UBA4951 sp002314915	79.2431	102	320	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:55:21,747] [INFO] GTDB search result was written to GCA_024408295.1_ASM2440829v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:55:21,748] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:55:21,751] [INFO] DFAST_QC result json was written to GCA_024408295.1_ASM2440829v1_genomic.fna/dqc_result.json
[2023-06-30 20:55:21,752] [INFO] DFAST_QC completed!
[2023-06-30 20:55:21,752] [INFO] Total running time: 0h0m30s