[2024-01-24 14:55:51,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference
[2024-01-24 14:55:52,316] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,317] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,317] [INFO] Running command: gunzip -c /var/lib/cwl/stga772c495-353b-4295-9a96-e28bf51e96c5/GCF_002243515.1_ASM224351v1_genomic.fna.gz | prodigal -d GCF_002243515.1_ASM224351v1_genomic.fna/cds.fna -a GCF_002243515.1_ASM224351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:10,435] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:10,435] [INFO] Task started: HMMsearch
[2024-01-24 14:56:10,435] [INFO] Running command: hmmsearch --tblout GCF_002243515.1_ASM224351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/reference_markers.hmm GCF_002243515.1_ASM224351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:10,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:10,750] [INFO] Found 6/6 markers.
[2024-01-24 14:56:10,787] [INFO] Query marker FASTA was written to GCF_002243515.1_ASM224351v1_genomic.fna/markers.fasta
[2024-01-24 14:56:10,788] [INFO] Task started: Blastn
[2024-01-24 14:56:10,788] [INFO] Running command: blastn -query GCF_002243515.1_ASM224351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/reference_markers.fasta -out GCF_002243515.1_ASM224351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:11,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:11,405] [INFO] Selected 27 target genomes.
[2024-01-24 14:56:11,406] [INFO] Target genome list was writen to GCF_002243515.1_ASM224351v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:11,418] [INFO] Task started: fastANI
[2024-01-24 14:56:11,418] [INFO] Running command: fastANI --query /var/lib/cwl/stga772c495-353b-4295-9a96-e28bf51e96c5/GCF_002243515.1_ASM224351v1_genomic.fna.gz --refList GCF_002243515.1_ASM224351v1_genomic.fna/target_genomes.txt --output GCF_002243515.1_ASM224351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:33,546] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:33,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:33,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:33,553] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:33,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:33,553] [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
Tumebacillus algifaecis	strain=THMBR28	GCA_002243515.1	1214604	1214604	type	True	100.0	1504	1505	95	conclusive
Tumebacillus avium	strain=AR23208	GCA_002162355.1	1903704	1903704	type	True	82.7388	980	1505	95	below_threshold
Tumebacillus permanentifrigoris	strain=DSM 18773	GCA_003148565.1	378543	378543	type	True	77.9805	264	1505	95	below_threshold
Tumebacillus amylolyticus	strain=ITR2	GCA_016722965.1	2801339	2801339	type	True	77.6879	262	1505	95	below_threshold
Tumebacillus flagellatus	strain=GST4	GCA_000714935.1	1157490	1157490	type	True	77.5564	282	1505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:33,555] [INFO] DFAST Taxonomy check result was written to GCF_002243515.1_ASM224351v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:33,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:33,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:33,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/checkm_data
[2024-01-24 14:56:33,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:33,604] [INFO] Task started: CheckM
[2024-01-24 14:56:33,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002243515.1_ASM224351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002243515.1_ASM224351v1_genomic.fna/checkm_input GCF_002243515.1_ASM224351v1_genomic.fna/checkm_result
[2024-01-24 14:57:30,406] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:30,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:30,430] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:30,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:30,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002243515.1_ASM224351v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:30,431] [INFO] Task started: Blastn
[2024-01-24 14:57:30,431] [INFO] Running command: blastn -query GCF_002243515.1_ASM224351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488f2135-14c0-4077-85f1-f70fe98488a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002243515.1_ASM224351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:31,262] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:31,265] [INFO] Selected 22 target genomes.
[2024-01-24 14:57:31,265] [INFO] Target genome list was writen to GCF_002243515.1_ASM224351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:31,285] [INFO] Task started: fastANI
[2024-01-24 14:57:31,286] [INFO] Running command: fastANI --query /var/lib/cwl/stga772c495-353b-4295-9a96-e28bf51e96c5/GCF_002243515.1_ASM224351v1_genomic.fna.gz --refList GCF_002243515.1_ASM224351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002243515.1_ASM224351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:49,764] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:49,776] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:49,777] [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_002243515.1	s__Tumebacillus_A algifaecis	100.0	1504	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002162355.1	s__Tumebacillus_A avium	82.6265	975	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340785.1	s__Tumebacillus_A sp004340785	82.1002	941	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148565.1	s__Tumebacillus permanentifrigoris	77.9886	259	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722965.1	s__Tumebacillus sp016722965	77.6945	260	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714935.1	s__Tumebacillus flagellatus	77.5307	284	1505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:49,778] [INFO] GTDB search result was written to GCF_002243515.1_ASM224351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:49,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:49,782] [INFO] DFAST_QC result json was written to GCF_002243515.1_ASM224351v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:49,783] [INFO] DFAST_QC completed!
[2024-01-24 14:57:49,783] [INFO] Total running time: 0h1m59s