[2024-01-24 12:14:48,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference
[2024-01-24 12:14:49,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:49,623] [INFO] Task started: Prodigal
[2024-01-24 12:14:49,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgae6a7e88-1bcb-48da-85cf-ec33d43ffa92/GCF_018967645.1_ASM1896764v1_genomic.fna.gz | prodigal -d GCF_018967645.1_ASM1896764v1_genomic.fna/cds.fna -a GCF_018967645.1_ASM1896764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:55,850] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:55,851] [INFO] Task started: HMMsearch
[2024-01-24 12:14:55,851] [INFO] Running command: hmmsearch --tblout GCF_018967645.1_ASM1896764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/reference_markers.hmm GCF_018967645.1_ASM1896764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:56,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:56,061] [INFO] Found 6/6 markers.
[2024-01-24 12:14:56,095] [INFO] Query marker FASTA was written to GCF_018967645.1_ASM1896764v1_genomic.fna/markers.fasta
[2024-01-24 12:14:56,095] [INFO] Task started: Blastn
[2024-01-24 12:14:56,096] [INFO] Running command: blastn -query GCF_018967645.1_ASM1896764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/reference_markers.fasta -out GCF_018967645.1_ASM1896764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,702] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:56,703] [INFO] Target genome list was writen to GCF_018967645.1_ASM1896764v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,709] [INFO] Task started: fastANI
[2024-01-24 12:14:56,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgae6a7e88-1bcb-48da-85cf-ec33d43ffa92/GCF_018967645.1_ASM1896764v1_genomic.fna.gz --refList GCF_018967645.1_ASM1896764v1_genomic.fna/target_genomes.txt --output GCF_018967645.1_ASM1896764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:06,663] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:06,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:06,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:06,669] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:06,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:06,669] [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
Allobacillus halotolerans	strain=LMG 24826	GCA_018967645.1	570278	570278	type	True	100.0	867	867	95	conclusive
Allobacillus saliphilus	strain=SKP8-2	GCA_018138385.1	2912308	2912308	type	True	87.8231	705	867	95	below_threshold
Allobacillus salarius	strain=SKP4-8	GCA_007559425.1	1955272	1955272	type	True	87.1867	683	867	95	below_threshold
Alkalibacillus haloalkaliphilus	strain=NBRC 103110	GCA_007991275.1	94136	94136	type	True	76.9848	73	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,671] [INFO] DFAST Taxonomy check result was written to GCF_018967645.1_ASM1896764v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:06,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:06,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:06,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/checkm_data
[2024-01-24 12:15:06,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:06,700] [INFO] Task started: CheckM
[2024-01-24 12:15:06,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018967645.1_ASM1896764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018967645.1_ASM1896764v1_genomic.fna/checkm_input GCF_018967645.1_ASM1896764v1_genomic.fna/checkm_result
[2024-01-24 12:15:32,201] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:32,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:32,217] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:32,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:32,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018967645.1_ASM1896764v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:32,218] [INFO] Task started: Blastn
[2024-01-24 12:15:32,218] [INFO] Running command: blastn -query GCF_018967645.1_ASM1896764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58407fb6-009b-4004-957a-a776b9e8bc71/dqc_reference/reference_markers_gtdb.fasta -out GCF_018967645.1_ASM1896764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:33,014] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:33,018] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:33,018] [INFO] Target genome list was writen to GCF_018967645.1_ASM1896764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:33,028] [INFO] Task started: fastANI
[2024-01-24 12:15:33,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgae6a7e88-1bcb-48da-85cf-ec33d43ffa92/GCF_018967645.1_ASM1896764v1_genomic.fna.gz --refList GCF_018967645.1_ASM1896764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018967645.1_ASM1896764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:42,608] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,614] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:42,614] [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_018967645.1	s__Allobacillus halotolerans	100.0	867	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	97.75	97.75	0.93	0.93	2	conclusive
GCF_018138385.1	s__Allobacillus sp018138385	87.8168	706	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559425.1	s__Allobacillus sp007559425	87.1867	683	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Allobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991275.1	s__Alkalibacillus haloalkaliphilus	77.0198	72	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Alkalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003843875.1	s__Aquisalibacillus elongatus	76.7036	72	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Aquisalibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,616] [INFO] GTDB search result was written to GCF_018967645.1_ASM1896764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:42,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:42,619] [INFO] DFAST_QC result json was written to GCF_018967645.1_ASM1896764v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:42,619] [INFO] DFAST_QC completed!
[2024-01-24 12:15:42,619] [INFO] Total running time: 0h0m54s