[2023-06-17 11:26:55,889] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:55,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:55,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg93bc2ec5-7885-462e-880d-7ad6aaf87dd7/dqc_reference
[2023-06-17 11:26:57,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:57,359] [INFO] Task started: Prodigal
[2023-06-17 11:26:57,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2ded61d-04f7-4e7c-adf6-9493e90d6faa/GCA_013330875.1_ASM1333087v1_genomic.fna.gz | prodigal -d GCA_013330875.1_ASM1333087v1_genomic.fna/cds.fna -a GCA_013330875.1_ASM1333087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:59,953] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:59,953] [INFO] Task started: HMMsearch
[2023-06-17 11:26:59,953] [INFO] Running command: hmmsearch --tblout GCA_013330875.1_ASM1333087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93bc2ec5-7885-462e-880d-7ad6aaf87dd7/dqc_reference/reference_markers.hmm GCA_013330875.1_ASM1333087v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:27:00,158] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:27:00,159] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc2ded61d-04f7-4e7c-adf6-9493e90d6faa/GCA_013330875.1_ASM1333087v1_genomic.fna.gz]
[2023-06-17 11:27:00,186] [INFO] Query marker FASTA was written to GCA_013330875.1_ASM1333087v1_genomic.fna/markers.fasta
[2023-06-17 11:27:00,187] [INFO] Task started: Blastn
[2023-06-17 11:27:00,187] [INFO] Running command: blastn -query GCA_013330875.1_ASM1333087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93bc2ec5-7885-462e-880d-7ad6aaf87dd7/dqc_reference/reference_markers.fasta -out GCA_013330875.1_ASM1333087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:00,690] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:00,694] [INFO] Selected 0 target genomes.
[2023-06-17 11:27:00,695] [INFO] Target genome list was writen to GCA_013330875.1_ASM1333087v1_genomic.fna/target_genomes.txt
[2023-06-17 11:27:00,695] [ERROR] File is empty. [GCA_013330875.1_ASM1333087v1_genomic.fna/target_genomes.txt]
[2023-06-17 11:27:00,695] [ERROR] Task failed. No target genome found.
[2023-06-17 11:27:00,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:27:00,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93bc2ec5-7885-462e-880d-7ad6aaf87dd7/dqc_reference/checkm_data
[2023-06-17 11:27:00,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:27:00,719] [INFO] Task started: CheckM
[2023-06-17 11:27:00,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013330875.1_ASM1333087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013330875.1_ASM1333087v1_genomic.fna/checkm_input GCA_013330875.1_ASM1333087v1_genomic.fna/checkm_result
[2023-06-17 11:27:18,677] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:18,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:18,701] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:18,701] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:18,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013330875.1_ASM1333087v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:18,702] [INFO] Task started: Blastn
[2023-06-17 11:27:18,702] [INFO] Running command: blastn -query GCA_013330875.1_ASM1333087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93bc2ec5-7885-462e-880d-7ad6aaf87dd7/dqc_reference/reference_markers_gtdb.fasta -out GCA_013330875.1_ASM1333087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:19,264] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:19,268] [INFO] Selected 4 target genomes.
[2023-06-17 11:27:19,268] [INFO] Target genome list was writen to GCA_013330875.1_ASM1333087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:19,272] [INFO] Task started: fastANI
[2023-06-17 11:27:19,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ded61d-04f7-4e7c-adf6-9493e90d6faa/GCA_013330875.1_ASM1333087v1_genomic.fna.gz --refList GCA_013330875.1_ASM1333087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013330875.1_ASM1333087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:20,140] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:20,145] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:27:20,145] [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_002686315.1	s__UBA11998 sp002686315	99.6348	184	305	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR9;g__UBA11998	95.0	99.63	99.63	0.60	0.60	2	conclusive
--------------------------------------------------------------------------------
[2023-06-17 11:27:20,148] [INFO] GTDB search result was written to GCA_013330875.1_ASM1333087v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:20,149] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:20,152] [INFO] DFAST_QC result json was written to GCA_013330875.1_ASM1333087v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:20,152] [INFO] DFAST_QC completed!
[2023-06-17 11:27:20,152] [INFO] Total running time: 0h0m24s