[2023-06-28 17:00:55,908] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:00:55,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:00:55,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference
[2023-06-28 17:00:57,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:00:57,313] [INFO] Task started: Prodigal
[2023-06-28 17:00:57,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg91a35c69-0a27-4cf4-aec9-989e8aae6ba2/GCA_027310185.1_ASM2731018v1_genomic.fna.gz | prodigal -d GCA_027310185.1_ASM2731018v1_genomic.fna/cds.fna -a GCA_027310185.1_ASM2731018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:01:01,589] [INFO] Task succeeded: Prodigal
[2023-06-28 17:01:01,590] [INFO] Task started: HMMsearch
[2023-06-28 17:01:01,590] [INFO] Running command: hmmsearch --tblout GCA_027310185.1_ASM2731018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/reference_markers.hmm GCA_027310185.1_ASM2731018v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:01:01,782] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:01:01,784] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg91a35c69-0a27-4cf4-aec9-989e8aae6ba2/GCA_027310185.1_ASM2731018v1_genomic.fna.gz]
[2023-06-28 17:01:01,807] [INFO] Query marker FASTA was written to GCA_027310185.1_ASM2731018v1_genomic.fna/markers.fasta
[2023-06-28 17:01:01,808] [INFO] Task started: Blastn
[2023-06-28 17:01:01,808] [INFO] Running command: blastn -query GCA_027310185.1_ASM2731018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/reference_markers.fasta -out GCA_027310185.1_ASM2731018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:02,283] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:02,287] [INFO] Selected 4 target genomes.
[2023-06-28 17:01:02,287] [INFO] Target genome list was writen to GCA_027310185.1_ASM2731018v1_genomic.fna/target_genomes.txt
[2023-06-28 17:01:02,289] [INFO] Task started: fastANI
[2023-06-28 17:01:02,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a35c69-0a27-4cf4-aec9-989e8aae6ba2/GCA_027310185.1_ASM2731018v1_genomic.fna.gz --refList GCA_027310185.1_ASM2731018v1_genomic.fna/target_genomes.txt --output GCA_027310185.1_ASM2731018v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:01:04,297] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:04,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:01:04,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:01:04,301] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:01:04,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:01:04,302] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Cuniculiplasma divulgatum	strain=S5(T) (=JCM 30642; =VKM B-2941)	GCA_900083515.1	1673428	1673428	type	True	82.4528	448	616	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:01:04,303] [INFO] DFAST Taxonomy check result was written to GCA_027310185.1_ASM2731018v1_genomic.fna/tc_result.tsv
[2023-06-28 17:01:04,304] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:01:04,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:01:04,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/checkm_data
[2023-06-28 17:01:04,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:01:04,331] [INFO] Task started: CheckM
[2023-06-28 17:01:04,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310185.1_ASM2731018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310185.1_ASM2731018v1_genomic.fna/checkm_input GCA_027310185.1_ASM2731018v1_genomic.fna/checkm_result
[2023-06-28 17:01:25,714] [INFO] Task succeeded: CheckM
[2023-06-28 17:01:25,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:01:25,738] [INFO] ===== Completeness check finished =====
[2023-06-28 17:01:25,739] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:01:25,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310185.1_ASM2731018v1_genomic.fna/markers.fasta)
[2023-06-28 17:01:25,739] [INFO] Task started: Blastn
[2023-06-28 17:01:25,739] [INFO] Running command: blastn -query GCA_027310185.1_ASM2731018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f499be7-8d77-4cec-8a68-03949ec02a45/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310185.1_ASM2731018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:26,169] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:26,173] [INFO] Selected 9 target genomes.
[2023-06-28 17:01:26,173] [INFO] Target genome list was writen to GCA_027310185.1_ASM2731018v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:01:26,206] [INFO] Task started: fastANI
[2023-06-28 17:01:26,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a35c69-0a27-4cf4-aec9-989e8aae6ba2/GCA_027310185.1_ASM2731018v1_genomic.fna.gz --refList GCA_027310185.1_ASM2731018v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310185.1_ASM2731018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:01:29,682] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:29,685] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:01:29,685] [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
GCF_900083515.1	s__Cuniculiplasma divulgatum	82.4528	448	616	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Cuniculiplasma	95.0	98.35	95.43	0.93	0.87	20	-
--------------------------------------------------------------------------------
[2023-06-28 17:01:29,691] [INFO] GTDB search result was written to GCA_027310185.1_ASM2731018v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:01:29,691] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:01:29,694] [INFO] DFAST_QC result json was written to GCA_027310185.1_ASM2731018v1_genomic.fna/dqc_result.json
[2023-06-28 17:01:29,695] [INFO] DFAST_QC completed!
[2023-06-28 17:01:29,695] [INFO] Total running time: 0h0m34s