[2023-06-13 07:44:09,786] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:44:09,791] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:44:09,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg30daf4cf-4ec9-4243-8d55-985bc26fa4af/dqc_reference
[2023-06-13 07:44:10,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:44:10,991] [INFO] Task started: Prodigal
[2023-06-13 07:44:10,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f9a4e1c-2ac7-4902-ad7d-9a3443a81a69/GCA_022449245.1_ASM2244924v1_genomic.fna.gz | prodigal -d GCA_022449245.1_ASM2244924v1_genomic.fna/cds.fna -a GCA_022449245.1_ASM2244924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:44:12,471] [INFO] Task succeeded: Prodigal
[2023-06-13 07:44:12,472] [INFO] Task started: HMMsearch
[2023-06-13 07:44:12,472] [INFO] Running command: hmmsearch --tblout GCA_022449245.1_ASM2244924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30daf4cf-4ec9-4243-8d55-985bc26fa4af/dqc_reference/reference_markers.hmm GCA_022449245.1_ASM2244924v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:44:12,724] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:44:12,726] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6f9a4e1c-2ac7-4902-ad7d-9a3443a81a69/GCA_022449245.1_ASM2244924v1_genomic.fna.gz]
[2023-06-13 07:44:12,743] [INFO] Query marker FASTA was written to GCA_022449245.1_ASM2244924v1_genomic.fna/markers.fasta
[2023-06-13 07:44:12,743] [INFO] Task started: Blastn
[2023-06-13 07:44:12,743] [INFO] Running command: blastn -query GCA_022449245.1_ASM2244924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30daf4cf-4ec9-4243-8d55-985bc26fa4af/dqc_reference/reference_markers.fasta -out GCA_022449245.1_ASM2244924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:44:13,239] [INFO] Task succeeded: Blastn
[2023-06-13 07:44:13,243] [INFO] Selected 0 target genomes.
[2023-06-13 07:44:13,243] [INFO] Target genome list was writen to GCA_022449245.1_ASM2244924v1_genomic.fna/target_genomes.txt
[2023-06-13 07:44:13,244] [ERROR] File is empty. [GCA_022449245.1_ASM2244924v1_genomic.fna/target_genomes.txt]
[2023-06-13 07:44:13,244] [ERROR] Task failed. No target genome found.
[2023-06-13 07:44:13,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:44:13,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30daf4cf-4ec9-4243-8d55-985bc26fa4af/dqc_reference/checkm_data
[2023-06-13 07:44:13,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:44:13,261] [INFO] Task started: CheckM
[2023-06-13 07:44:13,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449245.1_ASM2244924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449245.1_ASM2244924v1_genomic.fna/checkm_input GCA_022449245.1_ASM2244924v1_genomic.fna/checkm_result
[2023-06-13 07:44:26,910] [INFO] Task succeeded: CheckM
[2023-06-13 07:44:26,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 6.02%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:44:26,935] [INFO] ===== Completeness check finished =====
[2023-06-13 07:44:26,935] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:44:26,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449245.1_ASM2244924v1_genomic.fna/markers.fasta)
[2023-06-13 07:44:26,936] [INFO] Task started: Blastn
[2023-06-13 07:44:26,936] [INFO] Running command: blastn -query GCA_022449245.1_ASM2244924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30daf4cf-4ec9-4243-8d55-985bc26fa4af/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449245.1_ASM2244924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:44:27,387] [INFO] Task succeeded: Blastn
[2023-06-13 07:44:27,392] [INFO] Selected 3 target genomes.
[2023-06-13 07:44:27,392] [INFO] Target genome list was writen to GCA_022449245.1_ASM2244924v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:44:27,396] [INFO] Task started: fastANI
[2023-06-13 07:44:27,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f9a4e1c-2ac7-4902-ad7d-9a3443a81a69/GCA_022449245.1_ASM2244924v1_genomic.fna.gz --refList GCA_022449245.1_ASM2244924v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449245.1_ASM2244924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:44:27,999] [INFO] Task succeeded: fastANI
[2023-06-13 07:44:28,002] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 07:44:28,002] [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
--------------------------------------------------------------------------------
[2023-06-13 07:44:28,004] [INFO] GTDB search result was written to GCA_022449245.1_ASM2244924v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:44:28,004] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:44:28,006] [INFO] DFAST_QC result json was written to GCA_022449245.1_ASM2244924v1_genomic.fna/dqc_result.json
[2023-06-13 07:44:28,007] [INFO] DFAST_QC completed!
[2023-06-13 07:44:28,007] [INFO] Total running time: 0h0m18s