[2024-01-24 13:24:12,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference
[2024-01-24 13:24:13,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,528] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg569dbe60-7ac3-4cf2-8fca-a91c9a0317d9/GCF_000875975.1_ASM87597v1_genomic.fna.gz | prodigal -d GCF_000875975.1_ASM87597v1_genomic.fna/cds.fna -a GCF_000875975.1_ASM87597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:20,159] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:20,159] [INFO] Task started: HMMsearch
[2024-01-24 13:24:20,159] [INFO] Running command: hmmsearch --tblout GCF_000875975.1_ASM87597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/reference_markers.hmm GCF_000875975.1_ASM87597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:20,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:20,352] [INFO] Found 6/6 markers.
[2024-01-24 13:24:20,376] [INFO] Query marker FASTA was written to GCF_000875975.1_ASM87597v1_genomic.fna/markers.fasta
[2024-01-24 13:24:20,377] [INFO] Task started: Blastn
[2024-01-24 13:24:20,377] [INFO] Running command: blastn -query GCF_000875975.1_ASM87597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/reference_markers.fasta -out GCF_000875975.1_ASM87597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:20,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:20,971] [INFO] Selected 13 target genomes.
[2024-01-24 13:24:20,972] [INFO] Target genome list was writen to GCF_000875975.1_ASM87597v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:20,986] [INFO] Task started: fastANI
[2024-01-24 13:24:20,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg569dbe60-7ac3-4cf2-8fca-a91c9a0317d9/GCF_000875975.1_ASM87597v1_genomic.fna.gz --refList GCF_000875975.1_ASM87597v1_genomic.fna/target_genomes.txt --output GCF_000875975.1_ASM87597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:27,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:27,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:27,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:27,762] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:27,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:27,762] [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
Parachlamydia acanthamoebae	strain=Bn9	GCA_000875975.1	83552	83552	type	True	100.0	978	981	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:24:27,764] [INFO] DFAST Taxonomy check result was written to GCF_000875975.1_ASM87597v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:27,764] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:27,764] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:27,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/checkm_data
[2024-01-24 13:24:27,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:28,007] [INFO] Task started: CheckM
[2024-01-24 13:24:28,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000875975.1_ASM87597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000875975.1_ASM87597v1_genomic.fna/checkm_input GCF_000875975.1_ASM87597v1_genomic.fna/checkm_result
[2024-01-24 13:24:52,857] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:52,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:52,876] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:52,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:52,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000875975.1_ASM87597v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:52,877] [INFO] Task started: Blastn
[2024-01-24 13:24:52,877] [INFO] Running command: blastn -query GCF_000875975.1_ASM87597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d651a1f-e8ca-4b08-9451-365d6543d58d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000875975.1_ASM87597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:53,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:53,852] [INFO] Selected 19 target genomes.
[2024-01-24 13:24:53,852] [INFO] Target genome list was writen to GCF_000875975.1_ASM87597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:53,911] [INFO] Task started: fastANI
[2024-01-24 13:24:53,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg569dbe60-7ac3-4cf2-8fca-a91c9a0317d9/GCF_000875975.1_ASM87597v1_genomic.fna.gz --refList GCF_000875975.1_ASM87597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000875975.1_ASM87597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:01,982] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:01,985] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:01,985] [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_000875975.1	s__Parachlamydia acanthamoebae	100.0	978	981	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Parachlamydia	95.0	99.50	99.48	0.96	0.96	4	conclusive
GCF_018342475.1	s__Parachlamydia sp018342475	79.2939	335	981	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Parachlamydiaceae;g__Parachlamydia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:01,987] [INFO] GTDB search result was written to GCF_000875975.1_ASM87597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:01,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:01,989] [INFO] DFAST_QC result json was written to GCF_000875975.1_ASM87597v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:01,990] [INFO] DFAST_QC completed!
[2024-01-24 13:25:01,990] [INFO] Total running time: 0h0m50s