[2023-06-13 03:51:47,260] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:51:47,264] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:51:47,264] [INFO] DQC Reference Directory: /var/lib/cwl/stga9bbe14f-49f2-4623-9e22-ba7d365b4759/dqc_reference
[2023-06-13 03:51:48,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:51:48,930] [INFO] Task started: Prodigal
[2023-06-13 03:51:48,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg129bb257-3194-4a20-9e6a-b0e9cf5b6d33/GCA_022759165.1_ASM2275916v1_genomic.fna.gz | prodigal -d GCA_022759165.1_ASM2275916v1_genomic.fna/cds.fna -a GCA_022759165.1_ASM2275916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:51:51,099] [INFO] Task succeeded: Prodigal
[2023-06-13 03:51:51,099] [INFO] Task started: HMMsearch
[2023-06-13 03:51:51,100] [INFO] Running command: hmmsearch --tblout GCA_022759165.1_ASM2275916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9bbe14f-49f2-4623-9e22-ba7d365b4759/dqc_reference/reference_markers.hmm GCA_022759165.1_ASM2275916v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:51:51,293] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:51:51,294] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg129bb257-3194-4a20-9e6a-b0e9cf5b6d33/GCA_022759165.1_ASM2275916v1_genomic.fna.gz]
[2023-06-13 03:51:51,310] [INFO] Query marker FASTA was written to GCA_022759165.1_ASM2275916v1_genomic.fna/markers.fasta
[2023-06-13 03:51:51,310] [INFO] Task started: Blastn
[2023-06-13 03:51:51,310] [INFO] Running command: blastn -query GCA_022759165.1_ASM2275916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9bbe14f-49f2-4623-9e22-ba7d365b4759/dqc_reference/reference_markers.fasta -out GCA_022759165.1_ASM2275916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:51:53,205] [INFO] Task succeeded: Blastn
[2023-06-13 03:51:53,209] [INFO] Selected 0 target genomes.
[2023-06-13 03:51:53,209] [INFO] Target genome list was writen to GCA_022759165.1_ASM2275916v1_genomic.fna/target_genomes.txt
[2023-06-13 03:51:53,209] [ERROR] File is empty. [GCA_022759165.1_ASM2275916v1_genomic.fna/target_genomes.txt]
[2023-06-13 03:51:53,209] [ERROR] Task failed. No target genome found.
[2023-06-13 03:51:53,210] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:51:53,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9bbe14f-49f2-4623-9e22-ba7d365b4759/dqc_reference/checkm_data
[2023-06-13 03:51:53,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:51:53,231] [INFO] Task started: CheckM
[2023-06-13 03:51:53,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022759165.1_ASM2275916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022759165.1_ASM2275916v1_genomic.fna/checkm_input GCA_022759165.1_ASM2275916v1_genomic.fna/checkm_result
[2023-06-13 03:52:11,415] [INFO] Task succeeded: CheckM
[2023-06-13 03:52:11,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 03:52:11,451] [INFO] ===== Completeness check finished =====
[2023-06-13 03:52:11,452] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:52:11,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022759165.1_ASM2275916v1_genomic.fna/markers.fasta)
[2023-06-13 03:52:11,453] [INFO] Task started: Blastn
[2023-06-13 03:52:11,453] [INFO] Running command: blastn -query GCA_022759165.1_ASM2275916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9bbe14f-49f2-4623-9e22-ba7d365b4759/dqc_reference/reference_markers_gtdb.fasta -out GCA_022759165.1_ASM2275916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:52:11,961] [INFO] Task succeeded: Blastn
[2023-06-13 03:52:11,966] [INFO] Selected 1 target genomes.
[2023-06-13 03:52:11,966] [INFO] Target genome list was writen to GCA_022759165.1_ASM2275916v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:52:11,968] [INFO] Task started: fastANI
[2023-06-13 03:52:11,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg129bb257-3194-4a20-9e6a-b0e9cf5b6d33/GCA_022759165.1_ASM2275916v1_genomic.fna.gz --refList GCA_022759165.1_ASM2275916v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022759165.1_ASM2275916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:52:12,349] [INFO] Task succeeded: fastANI
[2023-06-13 03:52:12,352] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:52:12,353] [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_011333245.1	s__ARK-14 sp011333245	97.5364	234	345	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Fervidicoccaceae;g__ARK-14	95.0	97.70	97.70	0.65	0.65	2	conclusive
--------------------------------------------------------------------------------
[2023-06-13 03:52:12,355] [INFO] GTDB search result was written to GCA_022759165.1_ASM2275916v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:52:12,355] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:52:12,358] [INFO] DFAST_QC result json was written to GCA_022759165.1_ASM2275916v1_genomic.fna/dqc_result.json
[2023-06-13 03:52:12,358] [INFO] DFAST_QC completed!
[2023-06-13 03:52:12,358] [INFO] Total running time: 0h0m25s