[2024-01-24 13:01:24,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference
[2024-01-24 13:01:25,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,910] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bb90c7a-5f00-407f-a10b-7562f62b9c63/GCF_027925155.1_ASM2792515v1_genomic.fna.gz | prodigal -d GCF_027925155.1_ASM2792515v1_genomic.fna/cds.fna -a GCF_027925155.1_ASM2792515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,764] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,765] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,765] [INFO] Running command: hmmsearch --tblout GCF_027925155.1_ASM2792515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/reference_markers.hmm GCF_027925155.1_ASM2792515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,039] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,075] [INFO] Query marker FASTA was written to GCF_027925155.1_ASM2792515v1_genomic.fna/markers.fasta
[2024-01-24 13:01:34,075] [INFO] Task started: Blastn
[2024-01-24 13:01:34,075] [INFO] Running command: blastn -query GCF_027925155.1_ASM2792515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/reference_markers.fasta -out GCF_027925155.1_ASM2792515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,652] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:34,652] [INFO] Target genome list was writen to GCF_027925155.1_ASM2792515v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,660] [INFO] Task started: fastANI
[2024-01-24 13:01:34,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb90c7a-5f00-407f-a10b-7562f62b9c63/GCF_027925155.1_ASM2792515v1_genomic.fna.gz --refList GCF_027925155.1_ASM2792515v1_genomic.fna/target_genomes.txt --output GCF_027925155.1_ASM2792515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:41,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:41,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:41,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:41,385] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:41,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:41,386] [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
Ilyobacter polytropus	strain=DSM 2926	GCA_000165505.1	167642	167642	type	True	76.9952	109	1339	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	76.8809	86	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,387] [INFO] DFAST Taxonomy check result was written to GCF_027925155.1_ASM2792515v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:41,388] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:41,388] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:41,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/checkm_data
[2024-01-24 13:01:41,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:41,431] [INFO] Task started: CheckM
[2024-01-24 13:01:41,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027925155.1_ASM2792515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027925155.1_ASM2792515v1_genomic.fna/checkm_input GCF_027925155.1_ASM2792515v1_genomic.fna/checkm_result
[2024-01-24 13:02:09,923] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:09,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,945] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:09,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:09,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027925155.1_ASM2792515v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:09,946] [INFO] Task started: Blastn
[2024-01-24 13:02:09,946] [INFO] Running command: blastn -query GCF_027925155.1_ASM2792515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb5e65a-25ae-440b-b39d-84a7fe17a602/dqc_reference/reference_markers_gtdb.fasta -out GCF_027925155.1_ASM2792515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,766] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:10,766] [INFO] Target genome list was writen to GCF_027925155.1_ASM2792515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:10,797] [INFO] Task started: fastANI
[2024-01-24 13:02:10,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb90c7a-5f00-407f-a10b-7562f62b9c63/GCF_027925155.1_ASM2792515v1_genomic.fna.gz --refList GCF_027925155.1_ASM2792515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027925155.1_ASM2792515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:19,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:19,170] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:19,171] [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_000165505.1	s__Ilyobacter polytropus	76.9523	113	1339	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Ilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900683735.1	s__Fusobacterium_A ulcerans_A	76.8625	51	1339	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.86	98.73	0.94	0.93	4	-
GCF_000426625.1	s__Psychrilyobacter atlanticus	76.8552	87	1339	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356455.1	s__Fusobacterium_A varium_A	76.6156	51	1339	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.56	99.56	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,172] [INFO] GTDB search result was written to GCF_027925155.1_ASM2792515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:19,176] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:19,179] [INFO] DFAST_QC result json was written to GCF_027925155.1_ASM2792515v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:19,179] [INFO] DFAST_QC completed!
[2024-01-24 13:02:19,180] [INFO] Total running time: 0h0m55s