[2024-01-24 11:26:20,941] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,943] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference
[2024-01-24 11:26:22,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,159] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bc52908-9601-4add-bc8c-be00b20c6474/GCF_003369835.1_ASM336983v1_genomic.fna.gz | prodigal -d GCF_003369835.1_ASM336983v1_genomic.fna/cds.fna -a GCF_003369835.1_ASM336983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:42,285] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:42,286] [INFO] Task started: HMMsearch
[2024-01-24 11:26:42,286] [INFO] Running command: hmmsearch --tblout GCF_003369835.1_ASM336983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/reference_markers.hmm GCF_003369835.1_ASM336983v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:42,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:42,622] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3bc52908-9601-4add-bc8c-be00b20c6474/GCF_003369835.1_ASM336983v1_genomic.fna.gz]
[2024-01-24 11:26:42,662] [INFO] Query marker FASTA was written to GCF_003369835.1_ASM336983v1_genomic.fna/markers.fasta
[2024-01-24 11:26:42,663] [INFO] Task started: Blastn
[2024-01-24 11:26:42,663] [INFO] Running command: blastn -query GCF_003369835.1_ASM336983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/reference_markers.fasta -out GCF_003369835.1_ASM336983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:43,212] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:43,217] [INFO] Selected 8 target genomes.
[2024-01-24 11:26:43,217] [INFO] Target genome list was writen to GCF_003369835.1_ASM336983v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:43,225] [INFO] Task started: fastANI
[2024-01-24 11:26:43,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc52908-9601-4add-bc8c-be00b20c6474/GCF_003369835.1_ASM336983v1_genomic.fna.gz --refList GCF_003369835.1_ASM336983v1_genomic.fna/target_genomes.txt --output GCF_003369835.1_ASM336983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:52,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:52,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:52,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:52,034] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:52,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:52,034] [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
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	100.0	1453	1454	95	conclusive
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	83.4317	831	1454	95	below_threshold
Halorussus ruber	strain=YC25	GCA_004765785.1	1126238	1126238	type	True	83.3174	925	1454	95	below_threshold
Halorussus salinus	strain=YJ-37-H	GCA_004765815.2	1364935	1364935	type	True	83.3008	962	1454	95	below_threshold
Halorussus litoreus	strain=HD8-51	GCA_003382685.1	1710536	1710536	type	True	83.2151	825	1454	95	below_threshold
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	82.7788	797	1454	95	below_threshold
Halorussus pelagicus	strain=RC-68	GCA_004087835.1	2505977	2505977	type	True	82.7245	819	1454	95	below_threshold
Halorussus amylolyticus	strain=YC93	GCA_004143485.2	1126242	1126242	type	True	81.4828	783	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:52,036] [INFO] DFAST Taxonomy check result was written to GCF_003369835.1_ASM336983v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:52,036] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:52,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:52,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/checkm_data
[2024-01-24 11:26:52,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:52,078] [INFO] Task started: CheckM
[2024-01-24 11:26:52,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003369835.1_ASM336983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003369835.1_ASM336983v1_genomic.fna/checkm_input GCF_003369835.1_ASM336983v1_genomic.fna/checkm_result
[2024-01-24 11:27:46,307] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:46,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,331] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:46,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:46,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003369835.1_ASM336983v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:46,332] [INFO] Task started: Blastn
[2024-01-24 11:27:46,333] [INFO] Running command: blastn -query GCF_003369835.1_ASM336983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d830355-f254-4df7-bca0-52fd7e5c36d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003369835.1_ASM336983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:46,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:46,855] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:46,855] [INFO] Target genome list was writen to GCF_003369835.1_ASM336983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:46,865] [INFO] Task started: fastANI
[2024-01-24 11:27:46,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bc52908-9601-4add-bc8c-be00b20c6474/GCF_003369835.1_ASM336983v1_genomic.fna.gz --refList GCF_003369835.1_ASM336983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003369835.1_ASM336983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:56,638] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:56,652] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:56,653] [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_003369835.1	s__Halorussus rarus	100.0	1453	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010747475.1	s__Halorussus sp010747475	84.3064	980	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239435.1	s__Halorussus sp005239435	83.8757	991	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765805.1	s__Halorussus sp004765805	83.4546	830	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765785.1	s__Halorussus ruber	83.3171	925	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765815.2	s__Halorussus salinus	83.317	961	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765795.1	s__Halorussus sp004765795	82.7904	794	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	98.88	98.88	0.88	0.88	2	-
GCF_004087835.1	s__Halorussus sp004087835	82.7213	818	1454	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:56,654] [INFO] GTDB search result was written to GCF_003369835.1_ASM336983v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:56,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:56,658] [INFO] DFAST_QC result json was written to GCF_003369835.1_ASM336983v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:56,658] [INFO] DFAST_QC completed!
[2024-01-24 11:27:56,658] [INFO] Total running time: 0h1m36s