[2024-01-25 18:14:05,738] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference
[2024-01-25 18:14:06,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,843] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg0254b7da-60b1-481c-be78-cd80ccdd648e/GCF_003865175.1_ASM386517v1_genomic.fna.gz | prodigal -d GCF_003865175.1_ASM386517v1_genomic.fna/cds.fna -a GCF_003865175.1_ASM386517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:17,191] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:17,192] [INFO] Task started: HMMsearch
[2024-01-25 18:14:17,192] [INFO] Running command: hmmsearch --tblout GCF_003865175.1_ASM386517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/reference_markers.hmm GCF_003865175.1_ASM386517v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:17,398] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:17,399] [INFO] Found 6/6 markers.
[2024-01-25 18:14:17,422] [INFO] Query marker FASTA was written to GCF_003865175.1_ASM386517v1_genomic.fna/markers.fasta
[2024-01-25 18:14:17,422] [INFO] Task started: Blastn
[2024-01-25 18:14:17,422] [INFO] Running command: blastn -query GCF_003865175.1_ASM386517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/reference_markers.fasta -out GCF_003865175.1_ASM386517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:17,945] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:17,947] [INFO] Selected 19 target genomes.
[2024-01-25 18:14:17,948] [INFO] Target genome list was writen to GCF_003865175.1_ASM386517v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:17,949] [INFO] Task started: fastANI
[2024-01-25 18:14:17,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg0254b7da-60b1-481c-be78-cd80ccdd648e/GCF_003865175.1_ASM386517v1_genomic.fna.gz --refList GCF_003865175.1_ASM386517v1_genomic.fna/target_genomes.txt --output GCF_003865175.1_ASM386517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:29,422] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:29,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:29,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:29,427] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:29,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:29,427] [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
Schleiferia thermophila	strain=DSM 21410	GCA_003337435.1	884107	884107	type	True	99.9946	848	861	95	conclusive
Thermaurantimonas aggregans	strain=LA	GCA_003851885.1	2173829	2173829	type	True	76.9563	110	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:29,428] [INFO] DFAST Taxonomy check result was written to GCF_003865175.1_ASM386517v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:29,429] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:29,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:29,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/checkm_data
[2024-01-25 18:14:29,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:29,457] [INFO] Task started: CheckM
[2024-01-25 18:14:29,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003865175.1_ASM386517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003865175.1_ASM386517v1_genomic.fna/checkm_input GCF_003865175.1_ASM386517v1_genomic.fna/checkm_result
[2024-01-25 18:15:02,730] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:02,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:02,752] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:02,752] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:02,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003865175.1_ASM386517v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:02,752] [INFO] Task started: Blastn
[2024-01-25 18:15:02,752] [INFO] Running command: blastn -query GCF_003865175.1_ASM386517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12684a2f-8acf-43ea-88c7-9dd5d5fdc1ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003865175.1_ASM386517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:03,517] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:03,521] [INFO] Selected 24 target genomes.
[2024-01-25 18:15:03,521] [INFO] Target genome list was writen to GCF_003865175.1_ASM386517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:03,525] [INFO] Task started: fastANI
[2024-01-25 18:15:03,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg0254b7da-60b1-481c-be78-cd80ccdd648e/GCF_003865175.1_ASM386517v1_genomic.fna.gz --refList GCF_003865175.1_ASM386517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003865175.1_ASM386517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:16,747] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:16,750] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:16,750] [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_003337435.1	s__Schleiferia thermophila	99.9946	848	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Schleiferia	95.0	99.59	99.19	0.98	0.96	3	conclusive
GCF_003851885.1	s__Thermaurantimonas aggregans	76.9563	110	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Thermaurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:16,752] [INFO] GTDB search result was written to GCF_003865175.1_ASM386517v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:16,752] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:16,754] [INFO] DFAST_QC result json was written to GCF_003865175.1_ASM386517v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:16,754] [INFO] DFAST_QC completed!
[2024-01-25 18:15:16,754] [INFO] Total running time: 0h1m11s