[2023-06-19 04:14:50,896] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:50,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:50,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg65582aa3-f630-4c5e-afdc-1d40b5fd8eb0/dqc_reference
[2023-06-19 04:14:52,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:52,646] [INFO] Task started: Prodigal
[2023-06-19 04:14:52,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg5025a9eb-35f1-4666-9843-f0f44d6576a9/GCA_018303105.1_ASM1830310v1_genomic.fna.gz | prodigal -d GCA_018303105.1_ASM1830310v1_genomic.fna/cds.fna -a GCA_018303105.1_ASM1830310v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:59,490] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:59,490] [INFO] Task started: HMMsearch
[2023-06-19 04:14:59,490] [INFO] Running command: hmmsearch --tblout GCA_018303105.1_ASM1830310v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65582aa3-f630-4c5e-afdc-1d40b5fd8eb0/dqc_reference/reference_markers.hmm GCA_018303105.1_ASM1830310v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:59,676] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:59,677] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5025a9eb-35f1-4666-9843-f0f44d6576a9/GCA_018303105.1_ASM1830310v1_genomic.fna.gz]
[2023-06-19 04:14:59,704] [INFO] Query marker FASTA was written to GCA_018303105.1_ASM1830310v1_genomic.fna/markers.fasta
[2023-06-19 04:14:59,704] [INFO] Task started: Blastn
[2023-06-19 04:14:59,705] [INFO] Running command: blastn -query GCA_018303105.1_ASM1830310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65582aa3-f630-4c5e-afdc-1d40b5fd8eb0/dqc_reference/reference_markers.fasta -out GCA_018303105.1_ASM1830310v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:00,174] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:00,178] [INFO] Selected 0 target genomes.
[2023-06-19 04:15:00,179] [INFO] Target genome list was writen to GCA_018303105.1_ASM1830310v1_genomic.fna/target_genomes.txt
[2023-06-19 04:15:00,179] [ERROR] File is empty. [GCA_018303105.1_ASM1830310v1_genomic.fna/target_genomes.txt]
[2023-06-19 04:15:00,179] [ERROR] Task failed. No target genome found.
[2023-06-19 04:15:00,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:15:00,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65582aa3-f630-4c5e-afdc-1d40b5fd8eb0/dqc_reference/checkm_data
[2023-06-19 04:15:00,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:15:00,200] [INFO] Task started: CheckM
[2023-06-19 04:15:00,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018303105.1_ASM1830310v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018303105.1_ASM1830310v1_genomic.fna/checkm_input GCA_018303105.1_ASM1830310v1_genomic.fna/checkm_result
[2023-06-19 04:15:21,703] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:21,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:21,726] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:21,726] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:21,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018303105.1_ASM1830310v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:21,727] [INFO] Task started: Blastn
[2023-06-19 04:15:21,727] [INFO] Running command: blastn -query GCA_018303105.1_ASM1830310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65582aa3-f630-4c5e-afdc-1d40b5fd8eb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018303105.1_ASM1830310v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:22,173] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:22,184] [INFO] Selected 11 target genomes.
[2023-06-19 04:15:22,185] [INFO] Target genome list was writen to GCA_018303105.1_ASM1830310v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:22,191] [INFO] Task started: fastANI
[2023-06-19 04:15:22,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg5025a9eb-35f1-4666-9843-f0f44d6576a9/GCA_018303105.1_ASM1830310v1_genomic.fna.gz --refList GCA_018303105.1_ASM1830310v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018303105.1_ASM1830310v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:27,146] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:27,151] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:15:27,151] [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_018303105.1	s__JAGVYU01 sp018303105	99.9999	392	396	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__JAGVYU01;g__JAGVYU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 04:15:27,153] [INFO] GTDB search result was written to GCA_018303105.1_ASM1830310v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:27,154] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:27,156] [INFO] DFAST_QC result json was written to GCA_018303105.1_ASM1830310v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:27,156] [INFO] DFAST_QC completed!
[2023-06-19 04:15:27,156] [INFO] Total running time: 0h0m36s