[2024-01-24 14:15:34,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference
[2024-01-24 14:15:35,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,781] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgecef1b2a-6ae0-483b-a4d5-bbd77b85af23/GCF_002119425.1_ASM211942v1_genomic.fna.gz | prodigal -d GCF_002119425.1_ASM211942v1_genomic.fna/cds.fna -a GCF_002119425.1_ASM211942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:40,104] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:40,104] [INFO] Task started: HMMsearch
[2024-01-24 14:15:40,104] [INFO] Running command: hmmsearch --tblout GCF_002119425.1_ASM211942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/reference_markers.hmm GCF_002119425.1_ASM211942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:40,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:40,371] [INFO] Found 6/6 markers.
[2024-01-24 14:15:40,401] [INFO] Query marker FASTA was written to GCF_002119425.1_ASM211942v1_genomic.fna/markers.fasta
[2024-01-24 14:15:40,402] [INFO] Task started: Blastn
[2024-01-24 14:15:40,402] [INFO] Running command: blastn -query GCF_002119425.1_ASM211942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/reference_markers.fasta -out GCF_002119425.1_ASM211942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:41,037] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:41,040] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:41,041] [INFO] Target genome list was writen to GCF_002119425.1_ASM211942v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:41,069] [INFO] Task started: fastANI
[2024-01-24 14:15:41,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgecef1b2a-6ae0-483b-a4d5-bbd77b85af23/GCF_002119425.1_ASM211942v1_genomic.fna.gz --refList GCF_002119425.1_ASM211942v1_genomic.fna/target_genomes.txt --output GCF_002119425.1_ASM211942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:46,265] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:46,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:46,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:46,270] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:46,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:46,271] [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
Desulfurella amilsii	strain=TR1	GCA_002119425.1	1562698	1562698	type	True	100.0	649	658	95	conclusive
Desulfurella multipotens	strain=DSM 8415	GCA_900101285.1	79269	79269	type	True	79.6272	390	658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,272] [INFO] DFAST Taxonomy check result was written to GCF_002119425.1_ASM211942v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:46,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:46,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:46,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/checkm_data
[2024-01-24 14:15:46,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:46,297] [INFO] Task started: CheckM
[2024-01-24 14:15:46,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002119425.1_ASM211942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002119425.1_ASM211942v1_genomic.fna/checkm_input GCF_002119425.1_ASM211942v1_genomic.fna/checkm_result
[2024-01-24 14:16:06,980] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:06,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:07,005] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:07,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:07,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002119425.1_ASM211942v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:07,007] [INFO] Task started: Blastn
[2024-01-24 14:16:07,007] [INFO] Running command: blastn -query GCF_002119425.1_ASM211942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ecc1fd-a256-42b7-bc82-4a6eca9af687/dqc_reference/reference_markers_gtdb.fasta -out GCF_002119425.1_ASM211942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:07,785] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:07,790] [INFO] Selected 20 target genomes.
[2024-01-24 14:16:07,790] [INFO] Target genome list was writen to GCF_002119425.1_ASM211942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:07,861] [INFO] Task started: fastANI
[2024-01-24 14:16:07,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgecef1b2a-6ae0-483b-a4d5-bbd77b85af23/GCF_002119425.1_ASM211942v1_genomic.fna.gz --refList GCF_002119425.1_ASM211942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002119425.1_ASM211942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:13,996] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:14,000] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:14,001] [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_002119425.1	s__Desulfurella amilsii	100.0	649	658	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Desulfurellaceae;g__Desulfurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000517565.1	s__Desulfurella acetivorans	79.6632	402	658	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Desulfurellaceae;g__Desulfurella	95.0	99.07	98.86	0.97	0.96	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:14,006] [INFO] GTDB search result was written to GCF_002119425.1_ASM211942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:14,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:14,009] [INFO] DFAST_QC result json was written to GCF_002119425.1_ASM211942v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:14,009] [INFO] DFAST_QC completed!
[2024-01-24 14:16:14,009] [INFO] Total running time: 0h0m40s