[2023-06-28 12:17:34,440] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:17:34,443] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:17:34,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg80d6f887-2af9-4a8a-a3a4-d2056b50ccdf/dqc_reference
[2023-06-28 12:17:36,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:17:36,064] [INFO] Task started: Prodigal
[2023-06-28 12:17:36,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a86e205-1521-4af1-8b99-f33b9609a105/GCA_002708345.1_ASM270834v1_genomic.fna.gz | prodigal -d GCA_002708345.1_ASM270834v1_genomic.fna/cds.fna -a GCA_002708345.1_ASM270834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:17:41,271] [INFO] Task succeeded: Prodigal
[2023-06-28 12:17:41,272] [INFO] Task started: HMMsearch
[2023-06-28 12:17:41,272] [INFO] Running command: hmmsearch --tblout GCA_002708345.1_ASM270834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80d6f887-2af9-4a8a-a3a4-d2056b50ccdf/dqc_reference/reference_markers.hmm GCA_002708345.1_ASM270834v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:17:41,460] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:17:41,463] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8a86e205-1521-4af1-8b99-f33b9609a105/GCA_002708345.1_ASM270834v1_genomic.fna.gz]
[2023-06-28 12:17:41,489] [INFO] Query marker FASTA was written to GCA_002708345.1_ASM270834v1_genomic.fna/markers.fasta
[2023-06-28 12:17:41,490] [INFO] Task started: Blastn
[2023-06-28 12:17:41,490] [INFO] Running command: blastn -query GCA_002708345.1_ASM270834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d6f887-2af9-4a8a-a3a4-d2056b50ccdf/dqc_reference/reference_markers.fasta -out GCA_002708345.1_ASM270834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:17:41,986] [INFO] Task succeeded: Blastn
[2023-06-28 12:17:41,992] [INFO] Selected 0 target genomes.
[2023-06-28 12:17:41,993] [INFO] Target genome list was writen to GCA_002708345.1_ASM270834v1_genomic.fna/target_genomes.txt
[2023-06-28 12:17:41,993] [ERROR] File is empty. [GCA_002708345.1_ASM270834v1_genomic.fna/target_genomes.txt]
[2023-06-28 12:17:41,994] [ERROR] Task failed. No target genome found.
[2023-06-28 12:17:41,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:17:41,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80d6f887-2af9-4a8a-a3a4-d2056b50ccdf/dqc_reference/checkm_data
[2023-06-28 12:17:41,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:17:42,029] [INFO] Task started: CheckM
[2023-06-28 12:17:42,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708345.1_ASM270834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708345.1_ASM270834v1_genomic.fna/checkm_input GCA_002708345.1_ASM270834v1_genomic.fna/checkm_result
[2023-06-28 12:18:06,509] [INFO] Task succeeded: CheckM
[2023-06-28 12:18:06,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:18:06,531] [INFO] ===== Completeness check finished =====
[2023-06-28 12:18:06,532] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:18:06,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708345.1_ASM270834v1_genomic.fna/markers.fasta)
[2023-06-28 12:18:06,533] [INFO] Task started: Blastn
[2023-06-28 12:18:06,533] [INFO] Running command: blastn -query GCA_002708345.1_ASM270834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d6f887-2af9-4a8a-a3a4-d2056b50ccdf/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708345.1_ASM270834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:07,098] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:07,104] [INFO] Selected 5 target genomes.
[2023-06-28 12:18:07,104] [INFO] Target genome list was writen to GCA_002708345.1_ASM270834v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:18:07,107] [INFO] Task started: fastANI
[2023-06-28 12:18:07,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a86e205-1521-4af1-8b99-f33b9609a105/GCA_002708345.1_ASM270834v1_genomic.fna.gz --refList GCA_002708345.1_ASM270834v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708345.1_ASM270834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:18:12,353] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:12,358] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:18:12,359] [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_002708345.1	s__SAT2750 sp002708345	100.0	578	586	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SAT2750	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-28 12:18:12,361] [INFO] GTDB search result was written to GCA_002708345.1_ASM270834v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:18:12,362] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:18:12,364] [INFO] DFAST_QC result json was written to GCA_002708345.1_ASM270834v1_genomic.fna/dqc_result.json
[2023-06-28 12:18:12,364] [INFO] DFAST_QC completed!
[2023-06-28 12:18:12,364] [INFO] Total running time: 0h0m38s