[2023-06-19 15:25:43,994] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:25:44,000] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:25:44,000] [INFO] DQC Reference Directory: /var/lib/cwl/stge3d6d922-d45a-4164-b61e-0fb04ef2026e/dqc_reference
[2023-06-19 15:25:45,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:25:45,241] [INFO] Task started: Prodigal
[2023-06-19 15:25:45,241] [INFO] Running command: gunzip -c /var/lib/cwl/stgf75dab7d-f30c-4e24-9aea-bd6dfd3162e0/GCA_018238265.1_ASM1823826v1_genomic.fna.gz | prodigal -d GCA_018238265.1_ASM1823826v1_genomic.fna/cds.fna -a GCA_018238265.1_ASM1823826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:25:51,330] [INFO] Task succeeded: Prodigal
[2023-06-19 15:25:51,331] [INFO] Task started: HMMsearch
[2023-06-19 15:25:51,331] [INFO] Running command: hmmsearch --tblout GCA_018238265.1_ASM1823826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3d6d922-d45a-4164-b61e-0fb04ef2026e/dqc_reference/reference_markers.hmm GCA_018238265.1_ASM1823826v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:25:51,687] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:25:51,689] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf75dab7d-f30c-4e24-9aea-bd6dfd3162e0/GCA_018238265.1_ASM1823826v1_genomic.fna.gz]
[2023-06-19 15:25:51,724] [INFO] Query marker FASTA was written to GCA_018238265.1_ASM1823826v1_genomic.fna/markers.fasta
[2023-06-19 15:25:51,725] [INFO] Task started: Blastn
[2023-06-19 15:25:51,725] [INFO] Running command: blastn -query GCA_018238265.1_ASM1823826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3d6d922-d45a-4164-b61e-0fb04ef2026e/dqc_reference/reference_markers.fasta -out GCA_018238265.1_ASM1823826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:25:52,275] [INFO] Task succeeded: Blastn
[2023-06-19 15:25:52,278] [INFO] Selected 0 target genomes.
[2023-06-19 15:25:52,278] [INFO] Target genome list was writen to GCA_018238265.1_ASM1823826v1_genomic.fna/target_genomes.txt
[2023-06-19 15:25:52,279] [ERROR] File is empty. [GCA_018238265.1_ASM1823826v1_genomic.fna/target_genomes.txt]
[2023-06-19 15:25:52,279] [ERROR] Task failed. No target genome found.
[2023-06-19 15:25:52,279] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:25:52,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3d6d922-d45a-4164-b61e-0fb04ef2026e/dqc_reference/checkm_data
[2023-06-19 15:25:52,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:25:52,314] [INFO] Task started: CheckM
[2023-06-19 15:25:52,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018238265.1_ASM1823826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018238265.1_ASM1823826v1_genomic.fna/checkm_input GCA_018238265.1_ASM1823826v1_genomic.fna/checkm_result
[2023-06-19 15:26:20,364] [INFO] Task succeeded: CheckM
[2023-06-19 15:26:20,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 1.83%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-19 15:26:20,396] [INFO] ===== Completeness check finished =====
[2023-06-19 15:26:20,396] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:26:20,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018238265.1_ASM1823826v1_genomic.fna/markers.fasta)
[2023-06-19 15:26:20,397] [INFO] Task started: Blastn
[2023-06-19 15:26:20,397] [INFO] Running command: blastn -query GCA_018238265.1_ASM1823826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3d6d922-d45a-4164-b61e-0fb04ef2026e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018238265.1_ASM1823826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:26:20,951] [INFO] Task succeeded: Blastn
[2023-06-19 15:26:20,954] [INFO] Selected 4 target genomes.
[2023-06-19 15:26:20,954] [INFO] Target genome list was writen to GCA_018238265.1_ASM1823826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:26:20,957] [INFO] Task started: fastANI
[2023-06-19 15:26:20,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgf75dab7d-f30c-4e24-9aea-bd6dfd3162e0/GCA_018238265.1_ASM1823826v1_genomic.fna.gz --refList GCA_018238265.1_ASM1823826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018238265.1_ASM1823826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:26:23,765] [INFO] Task succeeded: fastANI
[2023-06-19 15:26:23,773] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:26:23,774] [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_018238825.1	s__MP8T-1 sp018238825	97.4615	547	792	d__Archaea;p__Asgardarchaeota;c__Thorarchaeia;o__Thorarchaeales;f__Thorarchaeaceae;g__MP8T-1	95.0	97.80	97.80	0.78	0.78	2	conclusive
GCA_018238205.1	s__MP8T-1 sp018238205	92.4425	634	792	d__Archaea;p__Asgardarchaeota;c__Thorarchaeia;o__Thorarchaeales;f__Thorarchaeaceae;g__MP8T-1	95.0	98.89	98.89	0.89	0.89	2	-
GCA_016840385.1	s__MP8T-1 sp016840385	80.2541	445	792	d__Archaea;p__Asgardarchaeota;c__Thorarchaeia;o__Thorarchaeales;f__Thorarchaeaceae;g__MP8T-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:26:23,776] [INFO] GTDB search result was written to GCA_018238265.1_ASM1823826v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:26:23,777] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:26:23,781] [INFO] DFAST_QC result json was written to GCA_018238265.1_ASM1823826v1_genomic.fna/dqc_result.json
[2023-06-19 15:26:23,781] [INFO] DFAST_QC completed!
[2023-06-19 15:26:23,781] [INFO] Total running time: 0h0m40s