[2024-01-24 12:23:35,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,863] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference
[2024-01-24 12:23:37,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:37,241] [INFO] Task started: Prodigal
[2024-01-24 12:23:37,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d5115f5-dc4b-48a6-aeb5-dd8fb6b6d7b9/GCF_021568795.1_ASM2156879v1_genomic.fna.gz | prodigal -d GCF_021568795.1_ASM2156879v1_genomic.fna/cds.fna -a GCF_021568795.1_ASM2156879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:43,955] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:43,956] [INFO] Task started: HMMsearch
[2024-01-24 12:23:43,956] [INFO] Running command: hmmsearch --tblout GCF_021568795.1_ASM2156879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/reference_markers.hmm GCF_021568795.1_ASM2156879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:44,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:44,212] [INFO] Found 6/6 markers.
[2024-01-24 12:23:44,241] [INFO] Query marker FASTA was written to GCF_021568795.1_ASM2156879v1_genomic.fna/markers.fasta
[2024-01-24 12:23:44,242] [INFO] Task started: Blastn
[2024-01-24 12:23:44,242] [INFO] Running command: blastn -query GCF_021568795.1_ASM2156879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/reference_markers.fasta -out GCF_021568795.1_ASM2156879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:44,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:44,831] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:44,831] [INFO] Target genome list was writen to GCF_021568795.1_ASM2156879v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:44,837] [INFO] Task started: fastANI
[2024-01-24 12:23:44,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5115f5-dc4b-48a6-aeb5-dd8fb6b6d7b9/GCF_021568795.1_ASM2156879v1_genomic.fna.gz --refList GCF_021568795.1_ASM2156879v1_genomic.fna/target_genomes.txt --output GCF_021568795.1_ASM2156879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:50,724] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:50,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:50,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:50,734] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:50,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:50,735] [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
Dethiosulfovibrio faecalis	strain=F2B	GCA_021568795.1	2720018	2720018	type	True	100.0	867	872	95	conclusive
Dethiosulfovibrio peptidovorans	strain=DSM 11002	GCA_000172975.1	47055	47055	type	True	92.3841	730	872	95	below_threshold
Dethiosulfovibrio salsuginis	strain=USBA 82	GCA_900177735.1	561720	561720	type	True	77.9228	236	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,737] [INFO] DFAST Taxonomy check result was written to GCF_021568795.1_ASM2156879v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:50,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:50,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:50,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/checkm_data
[2024-01-24 12:23:50,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:50,766] [INFO] Task started: CheckM
[2024-01-24 12:23:50,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021568795.1_ASM2156879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021568795.1_ASM2156879v1_genomic.fna/checkm_input GCF_021568795.1_ASM2156879v1_genomic.fna/checkm_result
[2024-01-24 12:24:15,966] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:15,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,989] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:15,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:15,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021568795.1_ASM2156879v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:15,991] [INFO] Task started: Blastn
[2024-01-24 12:24:15,991] [INFO] Running command: blastn -query GCF_021568795.1_ASM2156879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c48ab7-7f4c-4c4a-9d49-9067a4a9e93a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021568795.1_ASM2156879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:16,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:16,781] [INFO] Selected 17 target genomes.
[2024-01-24 12:24:16,781] [INFO] Target genome list was writen to GCF_021568795.1_ASM2156879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:16,796] [INFO] Task started: fastANI
[2024-01-24 12:24:16,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5115f5-dc4b-48a6-aeb5-dd8fb6b6d7b9/GCF_021568795.1_ASM2156879v1_genomic.fna.gz --refList GCF_021568795.1_ASM2156879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021568795.1_ASM2156879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:23,435] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:23,441] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:23,442] [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_000172975.1	s__Dethiosulfovibrio peptidovorans	92.3783	730	872	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177735.1	s__Dethiosulfovibrio salsuginis	77.9375	237	872	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748665.1	s__Dethiosulfovibrio peptidovorans_A	76.8778	70	872	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Dethiosulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:23,443] [INFO] GTDB search result was written to GCF_021568795.1_ASM2156879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:23,444] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:23,447] [INFO] DFAST_QC result json was written to GCF_021568795.1_ASM2156879v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:23,448] [INFO] DFAST_QC completed!
[2024-01-24 12:24:23,448] [INFO] Total running time: 0h0m48s