[2023-06-05 13:50:29,934] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:50:29,935] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:50:29,936] [INFO] DQC Reference Directory: /var/lib/cwl/stga525b6f1-c11a-4c2a-ac92-9f09f865322d/dqc_reference
[2023-06-05 13:50:31,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:50:31,702] [INFO] Task started: Prodigal
[2023-06-05 13:50:31,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg608b3cdd-1891-4a39-8025-7b2383fed559/GCA_010028525.1_ASM1002852v1_genomic.fna.gz | prodigal -d GCA_010028525.1_ASM1002852v1_genomic.fna/cds.fna -a GCA_010028525.1_ASM1002852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:50:35,043] [INFO] Task succeeded: Prodigal
[2023-06-05 13:50:35,044] [INFO] Task started: HMMsearch
[2023-06-05 13:50:35,044] [INFO] Running command: hmmsearch --tblout GCA_010028525.1_ASM1002852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga525b6f1-c11a-4c2a-ac92-9f09f865322d/dqc_reference/reference_markers.hmm GCA_010028525.1_ASM1002852v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:50:35,240] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:50:35,241] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg608b3cdd-1891-4a39-8025-7b2383fed559/GCA_010028525.1_ASM1002852v1_genomic.fna.gz]
[2023-06-05 13:50:35,267] [INFO] Query marker FASTA was written to GCA_010028525.1_ASM1002852v1_genomic.fna/markers.fasta
[2023-06-05 13:50:35,267] [INFO] Task started: Blastn
[2023-06-05 13:50:35,267] [INFO] Running command: blastn -query GCA_010028525.1_ASM1002852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga525b6f1-c11a-4c2a-ac92-9f09f865322d/dqc_reference/reference_markers.fasta -out GCA_010028525.1_ASM1002852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:50:35,699] [INFO] Task succeeded: Blastn
[2023-06-05 13:50:35,702] [INFO] Selected 0 target genomes.
[2023-06-05 13:50:35,702] [INFO] Target genome list was writen to GCA_010028525.1_ASM1002852v1_genomic.fna/target_genomes.txt
[2023-06-05 13:50:35,702] [ERROR] File is empty. [GCA_010028525.1_ASM1002852v1_genomic.fna/target_genomes.txt]
[2023-06-05 13:50:35,702] [ERROR] Task failed. No target genome found.
[2023-06-05 13:50:35,702] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:50:35,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga525b6f1-c11a-4c2a-ac92-9f09f865322d/dqc_reference/checkm_data
[2023-06-05 13:50:35,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:50:35,733] [INFO] Task started: CheckM
[2023-06-05 13:50:35,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010028525.1_ASM1002852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010028525.1_ASM1002852v1_genomic.fna/checkm_input GCA_010028525.1_ASM1002852v1_genomic.fna/checkm_result
[2023-06-05 13:50:52,762] [INFO] Task succeeded: CheckM
[2023-06-05 13:50:52,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 17.13%
Strain heterogeneity: 33.96%
--------------------------------------------------------------------------------
[2023-06-05 13:50:52,782] [INFO] ===== Completeness check finished =====
[2023-06-05 13:50:52,783] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:50:52,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010028525.1_ASM1002852v1_genomic.fna/markers.fasta)
[2023-06-05 13:50:52,783] [INFO] Task started: Blastn
[2023-06-05 13:50:52,783] [INFO] Running command: blastn -query GCA_010028525.1_ASM1002852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga525b6f1-c11a-4c2a-ac92-9f09f865322d/dqc_reference/reference_markers_gtdb.fasta -out GCA_010028525.1_ASM1002852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:50:53,181] [INFO] Task succeeded: Blastn
[2023-06-05 13:50:53,184] [INFO] Selected 3 target genomes.
[2023-06-05 13:50:53,184] [INFO] Target genome list was writen to GCA_010028525.1_ASM1002852v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:50:53,263] [INFO] Task started: fastANI
[2023-06-05 13:50:53,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg608b3cdd-1891-4a39-8025-7b2383fed559/GCA_010028525.1_ASM1002852v1_genomic.fna.gz --refList GCA_010028525.1_ASM1002852v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010028525.1_ASM1002852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:50:54,012] [INFO] Task succeeded: fastANI
[2023-06-05 13:50:54,014] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:50:54,014] [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_002728275.1	s__Kariarchaeum pelagius	96.486	141	297	d__Archaea;p__Asgardarchaeota;c__Heimdallarchaeia;o__UBA460;f__Kariarchaeaceae;g__Kariarchaeum	95.0	96.77	96.55	0.77	0.68	4	conclusive
--------------------------------------------------------------------------------
[2023-06-05 13:50:54,016] [INFO] GTDB search result was written to GCA_010028525.1_ASM1002852v1_genomic.fna/result_gtdb.tsv
[2023-06-05 13:50:54,016] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:50:54,018] [INFO] DFAST_QC result json was written to GCA_010028525.1_ASM1002852v1_genomic.fna/dqc_result.json
[2023-06-05 13:50:54,019] [INFO] DFAST_QC completed!
[2023-06-05 13:50:54,019] [INFO] Total running time: 0h0m24s