[2024-01-24 10:47:40,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,976] [INFO] DQC Reference Directory: /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,787] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg509ff1e1-cef8-4b13-b03c-b89ecf8649bf/GCF_007991335.1_ASM799133v1_genomic.fna.gz | prodigal -d GCF_007991335.1_ASM799133v1_genomic.fna/cds.fna -a GCF_007991335.1_ASM799133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:54,055] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:54,056] [INFO] Task started: HMMsearch
[2024-01-24 10:47:54,056] [INFO] Running command: hmmsearch --tblout GCF_007991335.1_ASM799133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/reference_markers.hmm GCF_007991335.1_ASM799133v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:54,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:54,330] [INFO] Found 6/6 markers.
[2024-01-24 10:47:54,366] [INFO] Query marker FASTA was written to GCF_007991335.1_ASM799133v1_genomic.fna/markers.fasta
[2024-01-24 10:47:54,367] [INFO] Task started: Blastn
[2024-01-24 10:47:54,367] [INFO] Running command: blastn -query GCF_007991335.1_ASM799133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/reference_markers.fasta -out GCF_007991335.1_ASM799133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:54,955] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:54,959] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:54,959] [INFO] Target genome list was writen to GCF_007991335.1_ASM799133v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:54,964] [INFO] Task started: fastANI
[2024-01-24 10:47:54,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg509ff1e1-cef8-4b13-b03c-b89ecf8649bf/GCF_007991335.1_ASM799133v1_genomic.fna.gz --refList GCF_007991335.1_ASM799133v1_genomic.fna/target_genomes.txt --output GCF_007991335.1_ASM799133v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:05,753] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:05,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:05,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:05,764] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:05,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:05,764] [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
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	100.0	1221	1225	95	conclusive
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	88.6636	1058	1225	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	88.6332	1067	1225	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	87.0402	1053	1225	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	80.7236	580	1225	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	80.1555	583	1225	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	78.9163	360	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,766] [INFO] DFAST Taxonomy check result was written to GCF_007991335.1_ASM799133v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:05,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:05,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:05,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/checkm_data
[2024-01-24 10:48:05,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:05,804] [INFO] Task started: CheckM
[2024-01-24 10:48:05,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991335.1_ASM799133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991335.1_ASM799133v1_genomic.fna/checkm_input GCF_007991335.1_ASM799133v1_genomic.fna/checkm_result
[2024-01-24 10:48:39,102] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:39,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:39,130] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:39,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:39,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991335.1_ASM799133v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:39,132] [INFO] Task started: Blastn
[2024-01-24 10:48:39,132] [INFO] Running command: blastn -query GCF_007991335.1_ASM799133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda1fbb9a-0b75-45fc-93a8-be524f3daaac/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991335.1_ASM799133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:39,915] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:39,919] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:39,919] [INFO] Target genome list was writen to GCF_007991335.1_ASM799133v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:39,925] [INFO] Task started: fastANI
[2024-01-24 10:48:39,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg509ff1e1-cef8-4b13-b03c-b89ecf8649bf/GCF_007991335.1_ASM799133v1_genomic.fna.gz --refList GCF_007991335.1_ASM799133v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991335.1_ASM799133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:48,588] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,601] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:48,602] [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_007991335.1	s__Halobacillus faecis	100.0	1221	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009856415.1	s__Halobacillus litoralis_C	88.7928	1072	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104185.1	s__Halobacillus aidingensis	88.6372	1066	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	96.52	96.52	0.91	0.91	2	-
GCF_009856445.1	s__Halobacillus litoralis	87.0384	1053	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_900108515.1	s__Halobacillus karajensis	80.7274	580	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.38	99.37	0.93	0.93	4	-
GCF_900114165.1	s__Halobacillus dabanensis	80.1292	586	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425705.1	s__Halobacillus kuroshimensis	78.9163	360	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	-
GCF_013694105.1	s__Halobacillus locisalis	78.5891	270	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,603] [INFO] GTDB search result was written to GCF_007991335.1_ASM799133v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:48,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:48,607] [INFO] DFAST_QC result json was written to GCF_007991335.1_ASM799133v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:48,607] [INFO] DFAST_QC completed!
[2024-01-24 10:48:48,607] [INFO] Total running time: 0h1m8s