[2023-06-29 20:05:50,227] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:05:50,231] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:05:50,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference
[2023-06-29 20:05:51,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:05:51,459] [INFO] Task started: Prodigal
[2023-06-29 20:05:51,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f90e039-c3d3-444a-92cc-2a9d133037bd/GCA_021832825.1_ASM2183282v1_genomic.fna.gz | prodigal -d GCA_021832825.1_ASM2183282v1_genomic.fna/cds.fna -a GCA_021832825.1_ASM2183282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:05:53,799] [INFO] Task succeeded: Prodigal
[2023-06-29 20:05:53,800] [INFO] Task started: HMMsearch
[2023-06-29 20:05:53,800] [INFO] Running command: hmmsearch --tblout GCA_021832825.1_ASM2183282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/reference_markers.hmm GCA_021832825.1_ASM2183282v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:05:54,013] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:05:54,014] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg9f90e039-c3d3-444a-92cc-2a9d133037bd/GCA_021832825.1_ASM2183282v1_genomic.fna.gz]
[2023-06-29 20:05:54,035] [INFO] Query marker FASTA was written to GCA_021832825.1_ASM2183282v1_genomic.fna/markers.fasta
[2023-06-29 20:05:54,036] [INFO] Task started: Blastn
[2023-06-29 20:05:54,036] [INFO] Running command: blastn -query GCA_021832825.1_ASM2183282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/reference_markers.fasta -out GCA_021832825.1_ASM2183282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:05:54,556] [INFO] Task succeeded: Blastn
[2023-06-29 20:05:54,560] [INFO] Selected 1 target genomes.
[2023-06-29 20:05:54,561] [INFO] Target genome list was writen to GCA_021832825.1_ASM2183282v1_genomic.fna/target_genomes.txt
[2023-06-29 20:05:54,562] [INFO] Task started: fastANI
[2023-06-29 20:05:54,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f90e039-c3d3-444a-92cc-2a9d133037bd/GCA_021832825.1_ASM2183282v1_genomic.fna.gz --refList GCA_021832825.1_ASM2183282v1_genomic.fna/target_genomes.txt --output GCA_021832825.1_ASM2183282v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:05:55,044] [INFO] Task succeeded: fastANI
[2023-06-29 20:05:55,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:05:55,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:05:55,048] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 20:05:55,048] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 20:05:55,048] [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	97.3468	204	316	95	conclusive
--------------------------------------------------------------------------------
[2023-06-29 20:05:55,050] [INFO] DFAST Taxonomy check result was written to GCA_021832825.1_ASM2183282v1_genomic.fna/tc_result.tsv
[2023-06-29 20:05:55,051] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:05:55,051] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:05:55,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/checkm_data
[2023-06-29 20:05:55,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:05:55,075] [INFO] Task started: CheckM
[2023-06-29 20:05:55,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021832825.1_ASM2183282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021832825.1_ASM2183282v1_genomic.fna/checkm_input GCA_021832825.1_ASM2183282v1_genomic.fna/checkm_result
[2023-06-29 20:06:10,925] [INFO] Task succeeded: CheckM
[2023-06-29 20:06:10,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:06:10,961] [INFO] ===== Completeness check finished =====
[2023-06-29 20:06:10,961] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:06:10,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021832825.1_ASM2183282v1_genomic.fna/markers.fasta)
[2023-06-29 20:06:10,962] [INFO] Task started: Blastn
[2023-06-29 20:06:10,962] [INFO] Running command: blastn -query GCA_021832825.1_ASM2183282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03634a96-1afe-47f8-aa0c-86fd2c90d7a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_021832825.1_ASM2183282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:11,434] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:11,441] [INFO] Selected 1 target genomes.
[2023-06-29 20:06:11,441] [INFO] Target genome list was writen to GCA_021832825.1_ASM2183282v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:06:11,442] [INFO] Task started: fastANI
[2023-06-29 20:06:11,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f90e039-c3d3-444a-92cc-2a9d133037bd/GCA_021832825.1_ASM2183282v1_genomic.fna.gz --refList GCA_021832825.1_ASM2183282v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021832825.1_ASM2183282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:06:11,870] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:11,875] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:06:11,876] [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	97.3468	204	316	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmataceae;g__Cuniculiplasma	95.0	98.35	95.43	0.93	0.87	20	conclusive
--------------------------------------------------------------------------------
[2023-06-29 20:06:11,879] [INFO] GTDB search result was written to GCA_021832825.1_ASM2183282v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:06:11,880] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:06:11,883] [INFO] DFAST_QC result json was written to GCA_021832825.1_ASM2183282v1_genomic.fna/dqc_result.json
[2023-06-29 20:06:11,883] [INFO] DFAST_QC completed!
[2023-06-29 20:06:11,883] [INFO] Total running time: 0h0m22s