[2024-01-24 11:05:19,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:19,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:19,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference
[2024-01-24 11:05:20,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:20,599] [INFO] Task started: Prodigal
[2024-01-24 11:05:20,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg42c98f3b-e9ae-4efd-8cd4-f03bddc0d253/GCF_016745835.1_ASM1674583v1_genomic.fna.gz | prodigal -d GCF_016745835.1_ASM1674583v1_genomic.fna/cds.fna -a GCF_016745835.1_ASM1674583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:29,168] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:29,169] [INFO] Task started: HMMsearch
[2024-01-24 11:05:29,169] [INFO] Running command: hmmsearch --tblout GCF_016745835.1_ASM1674583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/reference_markers.hmm GCF_016745835.1_ASM1674583v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:29,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:29,550] [INFO] Found 6/6 markers.
[2024-01-24 11:05:29,585] [INFO] Query marker FASTA was written to GCF_016745835.1_ASM1674583v1_genomic.fna/markers.fasta
[2024-01-24 11:05:29,586] [INFO] Task started: Blastn
[2024-01-24 11:05:29,586] [INFO] Running command: blastn -query GCF_016745835.1_ASM1674583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/reference_markers.fasta -out GCF_016745835.1_ASM1674583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:30,305] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:30,308] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:30,309] [INFO] Target genome list was writen to GCF_016745835.1_ASM1674583v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:30,319] [INFO] Task started: fastANI
[2024-01-24 11:05:30,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c98f3b-e9ae-4efd-8cd4-f03bddc0d253/GCF_016745835.1_ASM1674583v1_genomic.fna.gz --refList GCF_016745835.1_ASM1674583v1_genomic.fna/target_genomes.txt --output GCF_016745835.1_ASM1674583v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:47,268] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:47,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:47,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:47,273] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:47,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:47,273] [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
Caldalkalibacillus salinus	strain=YIM B00319	GCA_016745835.1	2803787	2803787	type	True	100.0	1226	1228	95	conclusive
Caldalkalibacillus mannanilyticus	strain=JCM 10596	GCA_000615945.1	1418	1418	type	True	76.2811	50	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:47,274] [INFO] DFAST Taxonomy check result was written to GCF_016745835.1_ASM1674583v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:47,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:47,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:47,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/checkm_data
[2024-01-24 11:05:47,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:47,314] [INFO] Task started: CheckM
[2024-01-24 11:05:47,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016745835.1_ASM1674583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016745835.1_ASM1674583v1_genomic.fna/checkm_input GCF_016745835.1_ASM1674583v1_genomic.fna/checkm_result
[2024-01-24 11:06:19,386] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:19,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,429] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:19,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:19,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016745835.1_ASM1674583v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:19,430] [INFO] Task started: Blastn
[2024-01-24 11:06:19,430] [INFO] Running command: blastn -query GCF_016745835.1_ASM1674583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95843f9a-27d1-4338-85dc-564671587f62/dqc_reference/reference_markers_gtdb.fasta -out GCF_016745835.1_ASM1674583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:20,527] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:20,530] [INFO] Selected 26 target genomes.
[2024-01-24 11:06:20,531] [INFO] Target genome list was writen to GCF_016745835.1_ASM1674583v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:20,550] [INFO] Task started: fastANI
[2024-01-24 11:06:20,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c98f3b-e9ae-4efd-8cd4-f03bddc0d253/GCF_016745835.1_ASM1674583v1_genomic.fna.gz --refList GCF_016745835.1_ASM1674583v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016745835.1_ASM1674583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:38,926] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:38,930] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:38,931] [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_016745835.1	s__YIM-B00319 sp016745835	100.0	1226	1228	d__Bacteria;p__Firmicutes;c__Bacilli;o__Caldalkalibacillales;f__JCM-10596;g__YIM-B00319	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:06:38,933] [INFO] GTDB search result was written to GCF_016745835.1_ASM1674583v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:38,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:38,936] [INFO] DFAST_QC result json was written to GCF_016745835.1_ASM1674583v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:38,937] [INFO] DFAST_QC completed!
[2024-01-24 11:06:38,937] [INFO] Total running time: 0h1m20s