[2023-06-17 07:11:51,608] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:11:51,610] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:11:51,611] [INFO] DQC Reference Directory: /var/lib/cwl/stgde40b4a2-83d5-40f2-8e4b-da4d19e90ffe/dqc_reference
[2023-06-17 07:11:52,817] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:11:52,818] [INFO] Task started: Prodigal
[2023-06-17 07:11:52,818] [INFO] Running command: gunzip -c /var/lib/cwl/stge28bd2e2-14be-455f-bc43-4e2edde53431/GCA_013330975.1_ASM1333097v1_genomic.fna.gz | prodigal -d GCA_013330975.1_ASM1333097v1_genomic.fna/cds.fna -a GCA_013330975.1_ASM1333097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:11:55,371] [INFO] Task succeeded: Prodigal
[2023-06-17 07:11:55,371] [INFO] Task started: HMMsearch
[2023-06-17 07:11:55,372] [INFO] Running command: hmmsearch --tblout GCA_013330975.1_ASM1333097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde40b4a2-83d5-40f2-8e4b-da4d19e90ffe/dqc_reference/reference_markers.hmm GCA_013330975.1_ASM1333097v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:11:55,539] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:11:55,541] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge28bd2e2-14be-455f-bc43-4e2edde53431/GCA_013330975.1_ASM1333097v1_genomic.fna.gz]
[2023-06-17 07:11:55,567] [INFO] Query marker FASTA was written to GCA_013330975.1_ASM1333097v1_genomic.fna/markers.fasta
[2023-06-17 07:11:55,568] [INFO] Task started: Blastn
[2023-06-17 07:11:55,568] [INFO] Running command: blastn -query GCA_013330975.1_ASM1333097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde40b4a2-83d5-40f2-8e4b-da4d19e90ffe/dqc_reference/reference_markers.fasta -out GCA_013330975.1_ASM1333097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:11:56,035] [INFO] Task succeeded: Blastn
[2023-06-17 07:11:56,040] [INFO] Selected 0 target genomes.
[2023-06-17 07:11:56,040] [INFO] Target genome list was writen to GCA_013330975.1_ASM1333097v1_genomic.fna/target_genomes.txt
[2023-06-17 07:11:56,040] [ERROR] File is empty. [GCA_013330975.1_ASM1333097v1_genomic.fna/target_genomes.txt]
[2023-06-17 07:11:56,041] [ERROR] Task failed. No target genome found.
[2023-06-17 07:11:56,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:11:56,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde40b4a2-83d5-40f2-8e4b-da4d19e90ffe/dqc_reference/checkm_data
[2023-06-17 07:11:56,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:11:56,060] [INFO] Task started: CheckM
[2023-06-17 07:11:56,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013330975.1_ASM1333097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013330975.1_ASM1333097v1_genomic.fna/checkm_input GCA_013330975.1_ASM1333097v1_genomic.fna/checkm_result
[2023-06-17 07:12:11,463] [INFO] Task succeeded: CheckM
[2023-06-17 07:12:11,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:12:11,487] [INFO] ===== Completeness check finished =====
[2023-06-17 07:12:11,487] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:12:11,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013330975.1_ASM1333097v1_genomic.fna/markers.fasta)
[2023-06-17 07:12:11,488] [INFO] Task started: Blastn
[2023-06-17 07:12:11,488] [INFO] Running command: blastn -query GCA_013330975.1_ASM1333097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde40b4a2-83d5-40f2-8e4b-da4d19e90ffe/dqc_reference/reference_markers_gtdb.fasta -out GCA_013330975.1_ASM1333097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:12:11,976] [INFO] Task succeeded: Blastn
[2023-06-17 07:12:12,010] [INFO] Selected 1 target genomes.
[2023-06-17 07:12:12,011] [INFO] Target genome list was writen to GCA_013330975.1_ASM1333097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:12:12,013] [INFO] Task started: fastANI
[2023-06-17 07:12:12,014] [INFO] Running command: fastANI --query /var/lib/cwl/stge28bd2e2-14be-455f-bc43-4e2edde53431/GCA_013330975.1_ASM1333097v1_genomic.fna.gz --refList GCA_013330975.1_ASM1333097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013330975.1_ASM1333097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:12:12,353] [INFO] Task succeeded: fastANI
[2023-06-17 07:12:12,358] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:12:12,358] [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_013330975.1	s__UBA11855 sp11852u	100.0	317	320	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__UBA233;g__UBA11855	95.0	98.96	98.96	0.77	0.77	2	conclusive
--------------------------------------------------------------------------------
[2023-06-17 07:12:12,360] [INFO] GTDB search result was written to GCA_013330975.1_ASM1333097v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:12:12,361] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:12:12,364] [INFO] DFAST_QC result json was written to GCA_013330975.1_ASM1333097v1_genomic.fna/dqc_result.json
[2023-06-17 07:12:12,364] [INFO] DFAST_QC completed!
[2023-06-17 07:12:12,364] [INFO] Total running time: 0h0m21s