[2024-01-25 19:58:05,391] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:05,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:05,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference
[2024-01-25 19:58:06,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:06,528] [INFO] Task started: Prodigal
[2024-01-25 19:58:06,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg01918aca-9dd7-4025-961c-5174a8195115/GCF_001027025.1_ASM102702v1_genomic.fna.gz | prodigal -d GCF_001027025.1_ASM102702v1_genomic.fna/cds.fna -a GCF_001027025.1_ASM102702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:11,134] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:11,135] [INFO] Task started: HMMsearch
[2024-01-25 19:58:11,135] [INFO] Running command: hmmsearch --tblout GCF_001027025.1_ASM102702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/reference_markers.hmm GCF_001027025.1_ASM102702v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:11,334] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:11,335] [INFO] Found 6/6 markers.
[2024-01-25 19:58:11,355] [INFO] Query marker FASTA was written to GCF_001027025.1_ASM102702v1_genomic.fna/markers.fasta
[2024-01-25 19:58:11,356] [INFO] Task started: Blastn
[2024-01-25 19:58:11,356] [INFO] Running command: blastn -query GCF_001027025.1_ASM102702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/reference_markers.fasta -out GCF_001027025.1_ASM102702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:11,880] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:11,883] [INFO] Selected 9 target genomes.
[2024-01-25 19:58:11,883] [INFO] Target genome list was writen to GCF_001027025.1_ASM102702v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:11,890] [INFO] Task started: fastANI
[2024-01-25 19:58:11,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg01918aca-9dd7-4025-961c-5174a8195115/GCF_001027025.1_ASM102702v1_genomic.fna.gz --refList GCF_001027025.1_ASM102702v1_genomic.fna/target_genomes.txt --output GCF_001027025.1_ASM102702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:17,581] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:17,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:17,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:17,586] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:17,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:17,586] [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
Kosmotoga pacifica	strain=SLHLJ1	GCA_001027025.1	1330330	1330330	type	True	100.0	723	723	95	conclusive
Kosmotoga olearia	strain=TBF 19.5.1	GCA_000023325.1	651457	651457	type	True	79.3146	94	723	95	below_threshold
Kosmotoga arenicorallina	strain=S304	GCA_001636545.1	688066	688066	type	True	78.1858	153	723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:17,588] [INFO] DFAST Taxonomy check result was written to GCF_001027025.1_ASM102702v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:17,588] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:17,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:17,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/checkm_data
[2024-01-25 19:58:17,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:17,614] [INFO] Task started: CheckM
[2024-01-25 19:58:17,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001027025.1_ASM102702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001027025.1_ASM102702v1_genomic.fna/checkm_input GCF_001027025.1_ASM102702v1_genomic.fna/checkm_result
[2024-01-25 19:58:36,956] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:36,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:36,973] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:36,973] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:36,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001027025.1_ASM102702v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:36,974] [INFO] Task started: Blastn
[2024-01-25 19:58:36,974] [INFO] Running command: blastn -query GCF_001027025.1_ASM102702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9301cfc6-71a4-4406-968b-2b03c35b51e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001027025.1_ASM102702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:37,714] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:37,717] [INFO] Selected 17 target genomes.
[2024-01-25 19:58:37,717] [INFO] Target genome list was writen to GCF_001027025.1_ASM102702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:37,736] [INFO] Task started: fastANI
[2024-01-25 19:58:37,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg01918aca-9dd7-4025-961c-5174a8195115/GCF_001027025.1_ASM102702v1_genomic.fna.gz --refList GCF_001027025.1_ASM102702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001027025.1_ASM102702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:46,009] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:46,013] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:46,013] [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_001027025.1	s__Kosmotoga_B pacifica	100.0	723	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Kosmotoga_B	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000023325.1	s__Kosmotoga olearia	79.4408	94	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Kosmotoga	95.0	98.80	98.80	0.93	0.93	2	-
GCF_001636545.1	s__Kosmotoga_B arenicorallina	78.1858	153	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Kosmotoga_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003643975.1	s__Kosmotoga_B sp003643975	77.8373	136	723	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Kosmotoga_B	95.0	99.27	99.27	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:46,014] [INFO] GTDB search result was written to GCF_001027025.1_ASM102702v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:46,015] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:46,017] [INFO] DFAST_QC result json was written to GCF_001027025.1_ASM102702v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:46,017] [INFO] DFAST_QC completed!
[2024-01-25 19:58:46,017] [INFO] Total running time: 0h0m41s