[2024-01-25 20:00:50,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:50,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:50,633] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference
[2024-01-25 20:00:51,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:51,767] [INFO] Task started: Prodigal
[2024-01-25 20:00:51,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f7fc634-10a2-418f-92ec-fa9ec314fe5f/GCF_000025285.1_ASM2528v1_genomic.fna.gz | prodigal -d GCF_000025285.1_ASM2528v1_genomic.fna/cds.fna -a GCF_000025285.1_ASM2528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:57,099] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:57,100] [INFO] Task started: HMMsearch
[2024-01-25 20:00:57,100] [INFO] Running command: hmmsearch --tblout GCF_000025285.1_ASM2528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/reference_markers.hmm GCF_000025285.1_ASM2528v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:57,296] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:57,298] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6f7fc634-10a2-418f-92ec-fa9ec314fe5f/GCF_000025285.1_ASM2528v1_genomic.fna.gz]
[2024-01-25 20:00:57,316] [INFO] Query marker FASTA was written to GCF_000025285.1_ASM2528v1_genomic.fna/markers.fasta
[2024-01-25 20:00:57,316] [INFO] Task started: Blastn
[2024-01-25 20:00:57,316] [INFO] Running command: blastn -query GCF_000025285.1_ASM2528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/reference_markers.fasta -out GCF_000025285.1_ASM2528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:57,768] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:57,770] [INFO] Selected 3 target genomes.
[2024-01-25 20:00:57,771] [INFO] Target genome list was writen to GCF_000025285.1_ASM2528v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:57,776] [INFO] Task started: fastANI
[2024-01-25 20:00:57,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f7fc634-10a2-418f-92ec-fa9ec314fe5f/GCF_000025285.1_ASM2528v1_genomic.fna.gz --refList GCF_000025285.1_ASM2528v1_genomic.fna/target_genomes.txt --output GCF_000025285.1_ASM2528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:59,254] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:59,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:59,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:59,258] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:59,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:59,258] [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
Archaeoglobus profundus	strain=DSM 5631	GCA_000025285.1	84156	84156	type	True	100.0	519	520	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:00:59,259] [INFO] DFAST Taxonomy check result was written to GCF_000025285.1_ASM2528v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:59,260] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:59,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:59,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/checkm_data
[2024-01-25 20:00:59,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:59,278] [INFO] Task started: CheckM
[2024-01-25 20:00:59,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025285.1_ASM2528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025285.1_ASM2528v1_genomic.fna/checkm_input GCF_000025285.1_ASM2528v1_genomic.fna/checkm_result
[2024-01-25 20:01:20,065] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:20,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:20,089] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:20,089] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:20,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025285.1_ASM2528v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:20,089] [INFO] Task started: Blastn
[2024-01-25 20:01:20,089] [INFO] Running command: blastn -query GCF_000025285.1_ASM2528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d21bd2-abad-4008-a0bf-cb9547befaf0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025285.1_ASM2528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:20,513] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:20,516] [INFO] Selected 9 target genomes.
[2024-01-25 20:01:20,516] [INFO] Target genome list was writen to GCF_000025285.1_ASM2528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:20,533] [INFO] Task started: fastANI
[2024-01-25 20:01:20,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f7fc634-10a2-418f-92ec-fa9ec314fe5f/GCF_000025285.1_ASM2528v1_genomic.fna.gz --refList GCF_000025285.1_ASM2528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025285.1_ASM2528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:24,386] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:24,389] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:24,389] [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_000025285.1	s__Archaeoglobus_B profundus	100.0	519	520	d__Archaea;p__Halobacteriota;c__Archaeoglobi;o__Archaeoglobales;f__Archaeoglobaceae;g__Archaeoglobus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:01:24,390] [INFO] GTDB search result was written to GCF_000025285.1_ASM2528v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:24,391] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:24,392] [INFO] DFAST_QC result json was written to GCF_000025285.1_ASM2528v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:24,392] [INFO] DFAST_QC completed!
[2024-01-25 20:01:24,392] [INFO] Total running time: 0h0m34s