[2023-06-13 01:40:06,539] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:40:06,543] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:40:06,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgb583cc86-5041-4e1d-be9a-4a1c350e9d07/dqc_reference
[2023-06-13 01:40:08,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:40:08,180] [INFO] Task started: Prodigal
[2023-06-13 01:40:08,181] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8daa64b-0ff3-4041-9a0b-4c54b0408110/GCA_022564585.1_ASM2256458v1_genomic.fna.gz | prodigal -d GCA_022564585.1_ASM2256458v1_genomic.fna/cds.fna -a GCA_022564585.1_ASM2256458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:40:17,898] [INFO] Task succeeded: Prodigal
[2023-06-13 01:40:17,898] [INFO] Task started: HMMsearch
[2023-06-13 01:40:17,898] [INFO] Running command: hmmsearch --tblout GCA_022564585.1_ASM2256458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb583cc86-5041-4e1d-be9a-4a1c350e9d07/dqc_reference/reference_markers.hmm GCA_022564585.1_ASM2256458v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:40:18,151] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:40:18,152] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc8daa64b-0ff3-4041-9a0b-4c54b0408110/GCA_022564585.1_ASM2256458v1_genomic.fna.gz]
[2023-06-13 01:40:18,189] [INFO] Query marker FASTA was written to GCA_022564585.1_ASM2256458v1_genomic.fna/markers.fasta
[2023-06-13 01:40:18,190] [INFO] Task started: Blastn
[2023-06-13 01:40:18,190] [INFO] Running command: blastn -query GCA_022564585.1_ASM2256458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb583cc86-5041-4e1d-be9a-4a1c350e9d07/dqc_reference/reference_markers.fasta -out GCA_022564585.1_ASM2256458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:18,701] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:18,705] [INFO] Selected 0 target genomes.
[2023-06-13 01:40:18,705] [INFO] Target genome list was writen to GCA_022564585.1_ASM2256458v1_genomic.fna/target_genomes.txt
[2023-06-13 01:40:18,705] [ERROR] File is empty. [GCA_022564585.1_ASM2256458v1_genomic.fna/target_genomes.txt]
[2023-06-13 01:40:18,706] [ERROR] Task failed. No target genome found.
[2023-06-13 01:40:18,706] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:40:18,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb583cc86-5041-4e1d-be9a-4a1c350e9d07/dqc_reference/checkm_data
[2023-06-13 01:40:18,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:40:18,749] [INFO] Task started: CheckM
[2023-06-13 01:40:18,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022564585.1_ASM2256458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022564585.1_ASM2256458v1_genomic.fna/checkm_input GCA_022564585.1_ASM2256458v1_genomic.fna/checkm_result
[2023-06-13 01:40:51,842] [INFO] Task succeeded: CheckM
[2023-06-13 01:40:51,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.23%
Contamintation: 8.68%
Strain heterogeneity: 27.27%
--------------------------------------------------------------------------------
[2023-06-13 01:40:51,875] [INFO] ===== Completeness check finished =====
[2023-06-13 01:40:51,876] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:40:51,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022564585.1_ASM2256458v1_genomic.fna/markers.fasta)
[2023-06-13 01:40:51,876] [INFO] Task started: Blastn
[2023-06-13 01:40:51,877] [INFO] Running command: blastn -query GCA_022564585.1_ASM2256458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb583cc86-5041-4e1d-be9a-4a1c350e9d07/dqc_reference/reference_markers_gtdb.fasta -out GCA_022564585.1_ASM2256458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:52,452] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:52,456] [INFO] Selected 4 target genomes.
[2023-06-13 01:40:52,457] [INFO] Target genome list was writen to GCA_022564585.1_ASM2256458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:40:52,460] [INFO] Task started: fastANI
[2023-06-13 01:40:52,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8daa64b-0ff3-4041-9a0b-4c54b0408110/GCA_022564585.1_ASM2256458v1_genomic.fna.gz --refList GCA_022564585.1_ASM2256458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022564585.1_ASM2256458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:40:55,456] [INFO] Task succeeded: fastANI
[2023-06-13 01:40:55,461] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:40:55,462] [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_016208685.1	s__JACQXM01 sp016208685	75.7152	52	831	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__UBA1845;g__JACQXM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:40:55,464] [INFO] GTDB search result was written to GCA_022564585.1_ASM2256458v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:40:55,465] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:40:55,469] [INFO] DFAST_QC result json was written to GCA_022564585.1_ASM2256458v1_genomic.fna/dqc_result.json
[2023-06-13 01:40:55,470] [INFO] DFAST_QC completed!
[2023-06-13 01:40:55,470] [INFO] Total running time: 0h0m49s