[2024-01-24 12:22:48,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference
[2024-01-24 12:22:49,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,277] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c52ef19-b3d4-4176-823f-8322d16ae0cb/GCF_000829445.1_ASM82944v1_genomic.fna.gz | prodigal -d GCF_000829445.1_ASM82944v1_genomic.fna/cds.fna -a GCF_000829445.1_ASM82944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:55,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:55,905] [INFO] Task started: HMMsearch
[2024-01-24 12:22:55,905] [INFO] Running command: hmmsearch --tblout GCF_000829445.1_ASM82944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/reference_markers.hmm GCF_000829445.1_ASM82944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:56,131] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:56,132] [INFO] Found 6/6 markers.
[2024-01-24 12:22:56,159] [INFO] Query marker FASTA was written to GCF_000829445.1_ASM82944v1_genomic.fna/markers.fasta
[2024-01-24 12:22:56,159] [INFO] Task started: Blastn
[2024-01-24 12:22:56,160] [INFO] Running command: blastn -query GCF_000829445.1_ASM82944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/reference_markers.fasta -out GCF_000829445.1_ASM82944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,703] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,707] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:56,707] [INFO] Target genome list was writen to GCF_000829445.1_ASM82944v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:56,723] [INFO] Task started: fastANI
[2024-01-24 12:22:56,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c52ef19-b3d4-4176-823f-8322d16ae0cb/GCF_000829445.1_ASM82944v1_genomic.fna.gz --refList GCF_000829445.1_ASM82944v1_genomic.fna/target_genomes.txt --output GCF_000829445.1_ASM82944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:04,480] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:04,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:04,486] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:04,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:04,487] [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
Jeotgalibacillus alimentarius	strain=YKJ-13	GCA_000829445.1	135826	135826	type	True	100.0	1102	1104	95	conclusive
Jeotgalibacillus terrae	strain=DSM 22174	GCA_016908195.1	587735	587735	type	True	91.6899	979	1104	95	below_threshold
Jeotgalibacillus malaysiensis	strain=D5	GCA_000818095.1	1508404	1508404	type	True	82.6334	704	1104	95	below_threshold
Jeotgalibacillus salarius	strain=ASL-1	GCA_004405125.1	546023	546023	type	True	81.6324	697	1104	95	below_threshold
Jeotgalibacillus aurantiacus	strain=T12	GCA_020595125.1	2763266	2763266	type	True	79.3163	370	1104	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	77.0401	53	1104	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.8463	50	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,488] [INFO] DFAST Taxonomy check result was written to GCF_000829445.1_ASM82944v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:04,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:04,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:04,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/checkm_data
[2024-01-24 12:23:04,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:04,523] [INFO] Task started: CheckM
[2024-01-24 12:23:04,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000829445.1_ASM82944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000829445.1_ASM82944v1_genomic.fna/checkm_input GCF_000829445.1_ASM82944v1_genomic.fna/checkm_result
[2024-01-24 12:23:29,599] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:29,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,619] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:29,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:29,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000829445.1_ASM82944v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:29,620] [INFO] Task started: Blastn
[2024-01-24 12:23:29,620] [INFO] Running command: blastn -query GCF_000829445.1_ASM82944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fefd645-e040-44fd-afcd-264e766d499e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000829445.1_ASM82944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:30,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:30,368] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:30,369] [INFO] Target genome list was writen to GCF_000829445.1_ASM82944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:30,383] [INFO] Task started: fastANI
[2024-01-24 12:23:30,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c52ef19-b3d4-4176-823f-8322d16ae0cb/GCF_000829445.1_ASM82944v1_genomic.fna.gz --refList GCF_000829445.1_ASM82944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000829445.1_ASM82944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:39,085] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:39,090] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:39,090] [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_000829445.1	s__Jeotgalibacillus alimentarius	100.0	1102	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016908195.1	s__Jeotgalibacillus terrae	91.6899	979	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818095.1	s__Jeotgalibacillus malaysiensis	82.6419	703	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004405125.1	s__Jeotgalibacillus salarius	81.6408	697	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004405105.1	s__Jeotgalibacillus sp004405105	79.0885	362	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Jeotgalibacillaceae;g__Jeotgalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163115.1	s__Mesobacillus selenatarsenatis_A	77.2827	56	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	76.7632	57	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:39,092] [INFO] GTDB search result was written to GCF_000829445.1_ASM82944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:39,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:39,094] [INFO] DFAST_QC result json was written to GCF_000829445.1_ASM82944v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:39,094] [INFO] DFAST_QC completed!
[2024-01-24 12:23:39,094] [INFO] Total running time: 0h0m51s