[2023-06-29 02:07:34,057] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:07:34,059] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:07:34,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference
[2023-06-29 02:07:35,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:07:35,324] [INFO] Task started: Prodigal
[2023-06-29 02:07:35,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ffde3e8-0dab-4bcc-a1da-0e1f51e9a168/GCA_027310895.1_ASM2731089v1_genomic.fna.gz | prodigal -d GCA_027310895.1_ASM2731089v1_genomic.fna/cds.fna -a GCA_027310895.1_ASM2731089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:07:41,800] [INFO] Task succeeded: Prodigal
[2023-06-29 02:07:41,800] [INFO] Task started: HMMsearch
[2023-06-29 02:07:41,801] [INFO] Running command: hmmsearch --tblout GCA_027310895.1_ASM2731089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/reference_markers.hmm GCA_027310895.1_ASM2731089v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:07:42,021] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:07:42,022] [INFO] Found 6/6 markers.
[2023-06-29 02:07:42,118] [INFO] Query marker FASTA was written to GCA_027310895.1_ASM2731089v1_genomic.fna/markers.fasta
[2023-06-29 02:07:42,118] [INFO] Task started: Blastn
[2023-06-29 02:07:42,118] [INFO] Running command: blastn -query GCA_027310895.1_ASM2731089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/reference_markers.fasta -out GCA_027310895.1_ASM2731089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:07:42,707] [INFO] Task succeeded: Blastn
[2023-06-29 02:07:42,712] [INFO] Selected 14 target genomes.
[2023-06-29 02:07:42,712] [INFO] Target genome list was writen to GCA_027310895.1_ASM2731089v1_genomic.fna/target_genomes.txt
[2023-06-29 02:07:42,722] [INFO] Task started: fastANI
[2023-06-29 02:07:42,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffde3e8-0dab-4bcc-a1da-0e1f51e9a168/GCA_027310895.1_ASM2731089v1_genomic.fna.gz --refList GCA_027310895.1_ASM2731089v1_genomic.fna/target_genomes.txt --output GCA_027310895.1_ASM2731089v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:07:51,910] [INFO] Task succeeded: fastANI
[2023-06-29 02:07:51,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:07:51,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:07:51,916] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:07:51,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:07:51,917] [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
Acidithrix ferrooxidans	strain=Py-F3	GCA_000949295.1	1280514	1280514	type	True	81.653	85	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:07:51,920] [INFO] DFAST Taxonomy check result was written to GCA_027310895.1_ASM2731089v1_genomic.fna/tc_result.tsv
[2023-06-29 02:07:51,921] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:07:51,921] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:07:51,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/checkm_data
[2023-06-29 02:07:51,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:07:51,969] [INFO] Task started: CheckM
[2023-06-29 02:07:51,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310895.1_ASM2731089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310895.1_ASM2731089v1_genomic.fna/checkm_input GCA_027310895.1_ASM2731089v1_genomic.fna/checkm_result
[2023-06-29 02:08:18,759] [INFO] Task succeeded: CheckM
[2023-06-29 02:08:18,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:08:18,789] [INFO] ===== Completeness check finished =====
[2023-06-29 02:08:18,789] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:08:18,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310895.1_ASM2731089v1_genomic.fna/markers.fasta)
[2023-06-29 02:08:18,790] [INFO] Task started: Blastn
[2023-06-29 02:08:18,790] [INFO] Running command: blastn -query GCA_027310895.1_ASM2731089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba91a583-554d-40cc-9da9-6b1a9b4b717b/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310895.1_ASM2731089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:08:19,627] [INFO] Task succeeded: Blastn
[2023-06-29 02:08:19,631] [INFO] Selected 19 target genomes.
[2023-06-29 02:08:19,631] [INFO] Target genome list was writen to GCA_027310895.1_ASM2731089v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:08:19,656] [INFO] Task started: fastANI
[2023-06-29 02:08:19,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffde3e8-0dab-4bcc-a1da-0e1f51e9a168/GCA_027310895.1_ASM2731089v1_genomic.fna.gz --refList GCA_027310895.1_ASM2731089v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310895.1_ASM2731089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:08:26,198] [INFO] Task succeeded: fastANI
[2023-06-29 02:08:26,203] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:08:26,203] [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_000949295.1	s__Acidithrix ferrooxidans	81.7764	86	877	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__Acidithrix	95.0	99.75	99.75	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-29 02:08:26,205] [INFO] GTDB search result was written to GCA_027310895.1_ASM2731089v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:08:26,206] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:08:26,210] [INFO] DFAST_QC result json was written to GCA_027310895.1_ASM2731089v1_genomic.fna/dqc_result.json
[2023-06-29 02:08:26,210] [INFO] DFAST_QC completed!
[2023-06-29 02:08:26,210] [INFO] Total running time: 0h0m52s