[2023-06-17 08:06:34,246] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:06:34,250] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:06:34,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference
[2023-06-17 08:06:35,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:06:35,633] [INFO] Task started: Prodigal
[2023-06-17 08:06:35,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg59540fe4-8cb7-4fc2-b5ef-473771df2b86/GCA_009778325.1_ASM977832v1_genomic.fna.gz | prodigal -d GCA_009778325.1_ASM977832v1_genomic.fna/cds.fna -a GCA_009778325.1_ASM977832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:06:40,555] [INFO] Task succeeded: Prodigal
[2023-06-17 08:06:40,555] [INFO] Task started: HMMsearch
[2023-06-17 08:06:40,556] [INFO] Running command: hmmsearch --tblout GCA_009778325.1_ASM977832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/reference_markers.hmm GCA_009778325.1_ASM977832v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:06:40,800] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:06:40,802] [INFO] Found 6/6 markers.
[2023-06-17 08:06:40,823] [INFO] Query marker FASTA was written to GCA_009778325.1_ASM977832v1_genomic.fna/markers.fasta
[2023-06-17 08:06:40,824] [INFO] Task started: Blastn
[2023-06-17 08:06:40,824] [INFO] Running command: blastn -query GCA_009778325.1_ASM977832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/reference_markers.fasta -out GCA_009778325.1_ASM977832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:06:41,475] [INFO] Task succeeded: Blastn
[2023-06-17 08:06:41,479] [INFO] Selected 13 target genomes.
[2023-06-17 08:06:41,480] [INFO] Target genome list was writen to GCA_009778325.1_ASM977832v1_genomic.fna/target_genomes.txt
[2023-06-17 08:06:41,511] [INFO] Task started: fastANI
[2023-06-17 08:06:41,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg59540fe4-8cb7-4fc2-b5ef-473771df2b86/GCA_009778325.1_ASM977832v1_genomic.fna.gz --refList GCA_009778325.1_ASM977832v1_genomic.fna/target_genomes.txt --output GCA_009778325.1_ASM977832v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:06:48,945] [INFO] Task succeeded: fastANI
[2023-06-17 08:06:48,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:06:48,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:06:48,949] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:06:48,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:06:48,950] [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
Endomicrobium proavitum	strain=Rsa215	GCA_001027545.1	1408281	1408281	type	True	77.1672	115	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:06:48,952] [INFO] DFAST Taxonomy check result was written to GCA_009778325.1_ASM977832v1_genomic.fna/tc_result.tsv
[2023-06-17 08:06:48,952] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:06:48,953] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:06:48,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/checkm_data
[2023-06-17 08:06:48,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:06:48,985] [INFO] Task started: CheckM
[2023-06-17 08:06:48,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009778325.1_ASM977832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009778325.1_ASM977832v1_genomic.fna/checkm_input GCA_009778325.1_ASM977832v1_genomic.fna/checkm_result
[2023-06-17 08:07:12,231] [INFO] Task succeeded: CheckM
[2023-06-17 08:07:12,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:07:12,261] [INFO] ===== Completeness check finished =====
[2023-06-17 08:07:12,261] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:07:12,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009778325.1_ASM977832v1_genomic.fna/markers.fasta)
[2023-06-17 08:07:12,262] [INFO] Task started: Blastn
[2023-06-17 08:07:12,262] [INFO] Running command: blastn -query GCA_009778325.1_ASM977832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e2f50f4-ad18-4b2d-9817-7c0486a9f1c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_009778325.1_ASM977832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:13,138] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:13,143] [INFO] Selected 13 target genomes.
[2023-06-17 08:07:13,144] [INFO] Target genome list was writen to GCA_009778325.1_ASM977832v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:07:13,148] [INFO] Task started: fastANI
[2023-06-17 08:07:13,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg59540fe4-8cb7-4fc2-b5ef-473771df2b86/GCA_009778325.1_ASM977832v1_genomic.fna.gz --refList GCA_009778325.1_ASM977832v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009778325.1_ASM977832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:07:18,598] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:18,615] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:07:18,615] [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
GCA_009778325.1	s__Endomicrobium sp009778325	100.0	765	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009776745.1	s__Endomicrobium sp009776745	80.1785	361	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781315.1	s__Endomicrobium sp009781315	78.2644	226	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.96	99.96	1.00	1.00	2	-
GCA_009778965.1	s__Endomicrobium sp009778965	77.9746	180	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	99.87	99.87	0.94	0.94	2	-
GCF_001027545.1	s__Endomicrobium proavitum	77.19	114	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__Endomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433245.1	s__JAHDRN01 sp018433245	75.9429	51	767	d__Bacteria;p__Elusimicrobiota;c__Endomicrobia;o__Endomicrobiales;f__Endomicrobiaceae;g__JAHDRN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:07:18,619] [INFO] GTDB search result was written to GCA_009778325.1_ASM977832v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:07:18,620] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:07:18,624] [INFO] DFAST_QC result json was written to GCA_009778325.1_ASM977832v1_genomic.fna/dqc_result.json
[2023-06-17 08:07:18,625] [INFO] DFAST_QC completed!
[2023-06-17 08:07:18,625] [INFO] Total running time: 0h0m44s