[2024-01-24 13:17:14,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,808] [INFO] DQC Reference Directory: /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference
[2024-01-24 13:17:16,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,251] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,252] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbc93cda-b2ed-4971-a766-6a59bd976a30/GCF_000010985.1_ASM1098v1_genomic.fna.gz | prodigal -d GCF_000010985.1_ASM1098v1_genomic.fna/cds.fna -a GCF_000010985.1_ASM1098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:20,984] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:20,985] [INFO] Task started: HMMsearch
[2024-01-24 13:17:20,985] [INFO] Running command: hmmsearch --tblout GCF_000010985.1_ASM1098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/reference_markers.hmm GCF_000010985.1_ASM1098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:21,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:21,282] [INFO] Found 6/6 markers.
[2024-01-24 13:17:21,309] [INFO] Query marker FASTA was written to GCF_000010985.1_ASM1098v1_genomic.fna/markers.fasta
[2024-01-24 13:17:21,309] [INFO] Task started: Blastn
[2024-01-24 13:17:21,309] [INFO] Running command: blastn -query GCF_000010985.1_ASM1098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/reference_markers.fasta -out GCF_000010985.1_ASM1098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:21,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:21,964] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:21,965] [INFO] Target genome list was writen to GCF_000010985.1_ASM1098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:21,972] [INFO] Task started: fastANI
[2024-01-24 13:17:21,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc93cda-b2ed-4971-a766-6a59bd976a30/GCF_000010985.1_ASM1098v1_genomic.fna.gz --refList GCF_000010985.1_ASM1098v1_genomic.fna/target_genomes.txt --output GCF_000010985.1_ASM1098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:30,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:30,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:30,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:30,516] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:30,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:30,516] [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
Deferribacter desulfuricans	strain=SSM1	GCA_000010985.1	197162	197162	type	True	100.0	846	846	95	conclusive
Deferribacter autotrophicus	strain=SL50	GCA_008362905.1	500465	500465	type	True	77.9053	253	846	95	below_threshold
Clostridioides difficile	strain=FDAARGOS_1525	GCA_020341515.1	1496	1496	type	True	74.9696	52	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:30,518] [INFO] DFAST Taxonomy check result was written to GCF_000010985.1_ASM1098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:30,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:30,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:30,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/checkm_data
[2024-01-24 13:17:30,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:30,550] [INFO] Task started: CheckM
[2024-01-24 13:17:30,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000010985.1_ASM1098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000010985.1_ASM1098v1_genomic.fna/checkm_input GCF_000010985.1_ASM1098v1_genomic.fna/checkm_result
[2024-01-24 13:17:51,531] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:51,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,548] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:51,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:51,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000010985.1_ASM1098v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:51,549] [INFO] Task started: Blastn
[2024-01-24 13:17:51,549] [INFO] Running command: blastn -query GCF_000010985.1_ASM1098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27ef9cd-acfb-4b9a-9408-25a4a54eca1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000010985.1_ASM1098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:52,523] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:52,528] [INFO] Selected 24 target genomes.
[2024-01-24 13:17:52,529] [INFO] Target genome list was writen to GCF_000010985.1_ASM1098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:52,588] [INFO] Task started: fastANI
[2024-01-24 13:17:52,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc93cda-b2ed-4971-a766-6a59bd976a30/GCF_000010985.1_ASM1098v1_genomic.fna.gz --refList GCF_000010985.1_ASM1098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000010985.1_ASM1098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:59,788] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,795] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:59,795] [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_000010985.1	s__Deferribacter desulfuricans	100.0	846	846	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Deferribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008362905.1	s__Deferribacter autotrophicus	77.9053	253	846	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Deferribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,797] [INFO] GTDB search result was written to GCF_000010985.1_ASM1098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:59,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:59,800] [INFO] DFAST_QC result json was written to GCF_000010985.1_ASM1098v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:59,800] [INFO] DFAST_QC completed!
[2024-01-24 13:17:59,801] [INFO] Total running time: 0h0m45s