[2023-06-29 12:22:08,709] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:22:08,711] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:22:08,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a9fa7e-1544-42db-b705-9fe23eddba79/dqc_reference
[2023-06-29 12:22:10,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:22:10,035] [INFO] Task started: Prodigal
[2023-06-29 12:22:10,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f04a203-e280-435b-97ef-dbf6256d1095/GCA_011772535.1_ASM1177253v1_genomic.fna.gz | prodigal -d GCA_011772535.1_ASM1177253v1_genomic.fna/cds.fna -a GCA_011772535.1_ASM1177253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:22:12,657] [INFO] Task succeeded: Prodigal
[2023-06-29 12:22:12,657] [INFO] Task started: HMMsearch
[2023-06-29 12:22:12,657] [INFO] Running command: hmmsearch --tblout GCA_011772535.1_ASM1177253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a9fa7e-1544-42db-b705-9fe23eddba79/dqc_reference/reference_markers.hmm GCA_011772535.1_ASM1177253v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:22:12,864] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:22:12,865] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8f04a203-e280-435b-97ef-dbf6256d1095/GCA_011772535.1_ASM1177253v1_genomic.fna.gz]
[2023-06-29 12:22:12,881] [INFO] Query marker FASTA was written to GCA_011772535.1_ASM1177253v1_genomic.fna/markers.fasta
[2023-06-29 12:22:12,881] [INFO] Task started: Blastn
[2023-06-29 12:22:12,881] [INFO] Running command: blastn -query GCA_011772535.1_ASM1177253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a9fa7e-1544-42db-b705-9fe23eddba79/dqc_reference/reference_markers.fasta -out GCA_011772535.1_ASM1177253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:13,400] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:13,404] [INFO] Selected 0 target genomes.
[2023-06-29 12:22:13,405] [INFO] Target genome list was writen to GCA_011772535.1_ASM1177253v1_genomic.fna/target_genomes.txt
[2023-06-29 12:22:13,405] [ERROR] File is empty. [GCA_011772535.1_ASM1177253v1_genomic.fna/target_genomes.txt]
[2023-06-29 12:22:13,405] [ERROR] Task failed. No target genome found.
[2023-06-29 12:22:13,405] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:13,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a9fa7e-1544-42db-b705-9fe23eddba79/dqc_reference/checkm_data
[2023-06-29 12:22:13,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:13,425] [INFO] Task started: CheckM
[2023-06-29 12:22:13,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011772535.1_ASM1177253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011772535.1_ASM1177253v1_genomic.fna/checkm_input GCA_011772535.1_ASM1177253v1_genomic.fna/checkm_result
[2023-06-29 12:22:29,780] [INFO] Task succeeded: CheckM
[2023-06-29 12:22:29,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:22:29,803] [INFO] ===== Completeness check finished =====
[2023-06-29 12:22:29,803] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:22:29,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011772535.1_ASM1177253v1_genomic.fna/markers.fasta)
[2023-06-29 12:22:29,804] [INFO] Task started: Blastn
[2023-06-29 12:22:29,804] [INFO] Running command: blastn -query GCA_011772535.1_ASM1177253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57a9fa7e-1544-42db-b705-9fe23eddba79/dqc_reference/reference_markers_gtdb.fasta -out GCA_011772535.1_ASM1177253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:30,314] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:30,319] [INFO] Selected 6 target genomes.
[2023-06-29 12:22:30,319] [INFO] Target genome list was writen to GCA_011772535.1_ASM1177253v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:22:30,325] [INFO] Task started: fastANI
[2023-06-29 12:22:30,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f04a203-e280-435b-97ef-dbf6256d1095/GCA_011772535.1_ASM1177253v1_genomic.fna.gz --refList GCA_011772535.1_ASM1177253v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011772535.1_ASM1177253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:22:31,224] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:31,227] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:22:31,227] [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_011773475.1	s__CS1-C013 sp011773475	85.4087	129	253	d__Archaea;p__Aenigmatarchaeota;c__Aenigmatarchaeia;o__Aenigmatarchaeales;f__Aenigmatarchaeaceae;g__CS1-C013	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:22:31,229] [INFO] GTDB search result was written to GCA_011772535.1_ASM1177253v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:22:31,230] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:22:31,232] [INFO] DFAST_QC result json was written to GCA_011772535.1_ASM1177253v1_genomic.fna/dqc_result.json
[2023-06-29 12:22:31,232] [INFO] DFAST_QC completed!
[2023-06-29 12:22:31,232] [INFO] Total running time: 0h0m23s