[2024-01-24 14:28:17,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference
[2024-01-24 14:28:20,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,488] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdf3f5de-1078-4dc4-959a-f9df0c91b7b9/GCF_021646685.1_ASM2164668v1_genomic.fna.gz | prodigal -d GCF_021646685.1_ASM2164668v1_genomic.fna/cds.fna -a GCF_021646685.1_ASM2164668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:31,273] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:31,274] [INFO] Task started: HMMsearch
[2024-01-24 14:28:31,274] [INFO] Running command: hmmsearch --tblout GCF_021646685.1_ASM2164668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/reference_markers.hmm GCF_021646685.1_ASM2164668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:31,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:31,590] [INFO] Found 6/6 markers.
[2024-01-24 14:28:31,641] [INFO] Query marker FASTA was written to GCF_021646685.1_ASM2164668v1_genomic.fna/markers.fasta
[2024-01-24 14:28:31,642] [INFO] Task started: Blastn
[2024-01-24 14:28:31,642] [INFO] Running command: blastn -query GCF_021646685.1_ASM2164668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/reference_markers.fasta -out GCF_021646685.1_ASM2164668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:32,316] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:32,320] [INFO] Selected 27 target genomes.
[2024-01-24 14:28:32,320] [INFO] Target genome list was writen to GCF_021646685.1_ASM2164668v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:32,335] [INFO] Task started: fastANI
[2024-01-24 14:28:32,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf3f5de-1078-4dc4-959a-f9df0c91b7b9/GCF_021646685.1_ASM2164668v1_genomic.fna.gz --refList GCF_021646685.1_ASM2164668v1_genomic.fna/target_genomes.txt --output GCF_021646685.1_ASM2164668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:49,901] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:49,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:49,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:49,910] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:49,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:49,910] [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
Pseudalkalibacillus berkeleyi	strain=KCTC 12718	GCA_021608225.1	1069813	1069813	type	True	78.5116	278	1421	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	77.885	239	1421	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.5503	52	1421	95	below_threshold
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	76.2337	55	1421	95	below_threshold
Alkalihalobacillus macyae	strain=DSM 16346	GCA_001039475.1	157733	157733	type	True	76.1341	50	1421	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	76.1112	57	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:49,911] [INFO] DFAST Taxonomy check result was written to GCF_021646685.1_ASM2164668v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:49,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:49,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:49,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/checkm_data
[2024-01-24 14:28:49,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:49,958] [INFO] Task started: CheckM
[2024-01-24 14:28:49,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021646685.1_ASM2164668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021646685.1_ASM2164668v1_genomic.fna/checkm_input GCF_021646685.1_ASM2164668v1_genomic.fna/checkm_result
[2024-01-24 14:29:27,467] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:27,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:27,492] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:27,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:27,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021646685.1_ASM2164668v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:27,493] [INFO] Task started: Blastn
[2024-01-24 14:29:27,493] [INFO] Running command: blastn -query GCF_021646685.1_ASM2164668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f2c232-4f34-45ec-9c20-6704b716fac0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021646685.1_ASM2164668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:28,337] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:28,342] [INFO] Selected 37 target genomes.
[2024-01-24 14:29:28,342] [INFO] Target genome list was writen to GCF_021646685.1_ASM2164668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:28,370] [INFO] Task started: fastANI
[2024-01-24 14:29:28,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf3f5de-1078-4dc4-959a-f9df0c91b7b9/GCF_021646685.1_ASM2164668v1_genomic.fna.gz --refList GCF_021646685.1_ASM2164668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021646685.1_ASM2164668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:53,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:53,263] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:29:53,263] [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_003259415.1	s__Metabacillus sp003259415	77.635	58	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	77.3326	50	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	76.5503	52	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613195.1	s__Mesobacillus sp018613195	76.437	51	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	98.95	98.95	0.85	0.85	2	-
GCF_001642935.1	s__Fictibacillus arsenicus_B	76.3464	57	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999465.1	s__Fictibacillus arsenicus	76.0642	56	1421	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:53,265] [INFO] GTDB search result was written to GCF_021646685.1_ASM2164668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:53,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:53,269] [INFO] DFAST_QC result json was written to GCF_021646685.1_ASM2164668v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:53,269] [INFO] DFAST_QC completed!
[2024-01-24 14:29:53,269] [INFO] Total running time: 0h1m35s