[2024-01-24 12:45:20,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference
[2024-01-24 12:45:21,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,840] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg52f32448-1e56-4145-82dd-569e0244f981/GCF_016937535.1_ASM1693753v1_genomic.fna.gz | prodigal -d GCF_016937535.1_ASM1693753v1_genomic.fna/cds.fna -a GCF_016937535.1_ASM1693753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:29,089] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:29,090] [INFO] Task started: HMMsearch
[2024-01-24 12:45:29,090] [INFO] Running command: hmmsearch --tblout GCF_016937535.1_ASM1693753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/reference_markers.hmm GCF_016937535.1_ASM1693753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:29,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:29,332] [INFO] Found 6/6 markers.
[2024-01-24 12:45:29,365] [INFO] Query marker FASTA was written to GCF_016937535.1_ASM1693753v1_genomic.fna/markers.fasta
[2024-01-24 12:45:29,366] [INFO] Task started: Blastn
[2024-01-24 12:45:29,366] [INFO] Running command: blastn -query GCF_016937535.1_ASM1693753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/reference_markers.fasta -out GCF_016937535.1_ASM1693753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:29,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:29,943] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:29,943] [INFO] Target genome list was writen to GCF_016937535.1_ASM1693753v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:29,964] [INFO] Task started: fastANI
[2024-01-24 12:45:29,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg52f32448-1e56-4145-82dd-569e0244f981/GCF_016937535.1_ASM1693753v1_genomic.fna.gz --refList GCF_016937535.1_ASM1693753v1_genomic.fna/target_genomes.txt --output GCF_016937535.1_ASM1693753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:35,338] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:35,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:35,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:35,346] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:35,347] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:35,347] [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
Sulfurospirillum deleyianum	strain=DSM 6946	GCA_000024885.1	65553	65553	type	True	76.332	58	792	95	below_threshold
Sulfurospirillum halorespirans	strain=DSM 13726; PCE-M2	GCA_001723605.1	194424	194424	type	True	76.159	61	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:35,349] [INFO] DFAST Taxonomy check result was written to GCF_016937535.1_ASM1693753v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:35,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:35,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:35,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/checkm_data
[2024-01-24 12:45:35,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:35,386] [INFO] Task started: CheckM
[2024-01-24 12:45:35,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016937535.1_ASM1693753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016937535.1_ASM1693753v1_genomic.fna/checkm_input GCF_016937535.1_ASM1693753v1_genomic.fna/checkm_result
[2024-01-24 12:46:01,713] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:01,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:01,869] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:01,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:01,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016937535.1_ASM1693753v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:01,870] [INFO] Task started: Blastn
[2024-01-24 12:46:01,870] [INFO] Running command: blastn -query GCF_016937535.1_ASM1693753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1a1ca9-df29-4995-90ea-95bd3b26979c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016937535.1_ASM1693753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:02,630] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:02,634] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:02,634] [INFO] Target genome list was writen to GCF_016937535.1_ASM1693753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:02,657] [INFO] Task started: fastANI
[2024-01-24 12:46:02,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg52f32448-1e56-4145-82dd-569e0244f981/GCF_016937535.1_ASM1693753v1_genomic.fna.gz --refList GCF_016937535.1_ASM1693753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016937535.1_ASM1693753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:08,676] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:08,681] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:08,681] [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_016937535.1	s__Kmv14 sp016937535	100.0	785	792	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__UBA1877;g__Kmv14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859645.1	s__Kmv14 sp014859645	85.2645	547	792	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__UBA1877;g__Kmv14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000743525.1	s__Sulfurospirillum sp000743525	76.4806	64	792	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002352945.1	s__UBA1877 sp002352945	76.4245	73	792	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__UBA1877;g__UBA1877	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:08,683] [INFO] GTDB search result was written to GCF_016937535.1_ASM1693753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:08,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:08,686] [INFO] DFAST_QC result json was written to GCF_016937535.1_ASM1693753v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:08,686] [INFO] DFAST_QC completed!
[2024-01-24 12:46:08,686] [INFO] Total running time: 0h0m48s