[2024-01-24 13:49:30,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference
[2024-01-24 13:49:31,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,707] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg502ce638-9ab5-4b20-a29f-1b10b785e9c1/GCF_014836955.1_ASM1483695v1_genomic.fna.gz | prodigal -d GCF_014836955.1_ASM1483695v1_genomic.fna/cds.fna -a GCF_014836955.1_ASM1483695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:43,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:43,004] [INFO] Task started: HMMsearch
[2024-01-24 13:49:43,004] [INFO] Running command: hmmsearch --tblout GCF_014836955.1_ASM1483695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/reference_markers.hmm GCF_014836955.1_ASM1483695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,374] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,415] [INFO] Query marker FASTA was written to GCF_014836955.1_ASM1483695v1_genomic.fna/markers.fasta
[2024-01-24 13:49:43,415] [INFO] Task started: Blastn
[2024-01-24 13:49:43,416] [INFO] Running command: blastn -query GCF_014836955.1_ASM1483695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/reference_markers.fasta -out GCF_014836955.1_ASM1483695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,028] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:44,028] [INFO] Target genome list was writen to GCF_014836955.1_ASM1483695v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:44,041] [INFO] Task started: fastANI
[2024-01-24 13:49:44,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg502ce638-9ab5-4b20-a29f-1b10b785e9c1/GCF_014836955.1_ASM1483695v1_genomic.fna.gz --refList GCF_014836955.1_ASM1483695v1_genomic.fna/target_genomes.txt --output GCF_014836955.1_ASM1483695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,167] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:01,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:01,167] [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
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	82.3661	765	1509	95	below_threshold
Siminovitchia fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	82.1886	905	1509	95	below_threshold
Siminovitchia acidinfaciens	strain=3-2-2	GCA_003605385.2	2321395	2321395	type	True	79.9716	662	1509	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.1881	55	1509	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	77.0495	93	1509	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	76.9986	70	1509	95	below_threshold
Weizmannia ginsengihumi	strain=Gsoil 114	GCA_011008565.1	363870	363870	type	True	76.9317	53	1509	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_011008805.1	157838	157838	type	True	76.885	69	1509	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.6576	51	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,169] [INFO] DFAST Taxonomy check result was written to GCF_014836955.1_ASM1483695v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/checkm_data
[2024-01-24 13:50:01,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,221] [INFO] Task started: CheckM
[2024-01-24 13:50:01,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836955.1_ASM1483695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836955.1_ASM1483695v1_genomic.fna/checkm_input GCF_014836955.1_ASM1483695v1_genomic.fna/checkm_result
[2024-01-24 13:50:39,805] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:39,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,828] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:39,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:39,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836955.1_ASM1483695v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:39,830] [INFO] Task started: Blastn
[2024-01-24 13:50:39,830] [INFO] Running command: blastn -query GCF_014836955.1_ASM1483695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg707731d0-88bc-41e4-b1d1-b65eb53f1099/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836955.1_ASM1483695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:40,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:40,620] [INFO] Selected 5 target genomes.
[2024-01-24 13:50:40,620] [INFO] Target genome list was writen to GCF_014836955.1_ASM1483695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:40,624] [INFO] Task started: fastANI
[2024-01-24 13:50:40,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg502ce638-9ab5-4b20-a29f-1b10b785e9c1/GCF_014836955.1_ASM1483695v1_genomic.fna.gz --refList GCF_014836955.1_ASM1483695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836955.1_ASM1483695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:46,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:46,969] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:46,969] [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_014836955.1	s__Siminovitchia sp014836955	100.0	1504	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009928435.1	s__Siminovitchia sp009928435	92.9971	978	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605405.2	s__Siminovitchia terrae	90.3818	1243	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.14	99.09	0.90	0.90	3	-
GCF_003605365.2	s__Siminovitchia fortis	82.3742	765	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.09	98.04	0.87	0.87	16	-
GCF_000374565.1	s__Siminovitchia fordii	82.2054	903	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.95	97.34	0.95	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:46,971] [INFO] GTDB search result was written to GCF_014836955.1_ASM1483695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:46,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:46,976] [INFO] DFAST_QC result json was written to GCF_014836955.1_ASM1483695v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:46,977] [INFO] DFAST_QC completed!
[2024-01-24 13:50:46,977] [INFO] Total running time: 0h1m17s