[2024-01-24 13:54:10,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:10,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:10,887] [INFO] DQC Reference Directory: /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference
[2024-01-24 13:54:12,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:12,207] [INFO] Task started: Prodigal
[2024-01-24 13:54:12,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fba8f7f-765f-4daa-8cf7-073a490fac33/GCF_000385175.1_ASM38517v1_genomic.fna.gz | prodigal -d GCF_000385175.1_ASM38517v1_genomic.fna/cds.fna -a GCF_000385175.1_ASM38517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:18,910] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:18,911] [INFO] Task started: HMMsearch
[2024-01-24 13:54:18,911] [INFO] Running command: hmmsearch --tblout GCF_000385175.1_ASM38517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/reference_markers.hmm GCF_000385175.1_ASM38517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:19,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:19,209] [INFO] Found 6/6 markers.
[2024-01-24 13:54:19,238] [INFO] Query marker FASTA was written to GCF_000385175.1_ASM38517v1_genomic.fna/markers.fasta
[2024-01-24 13:54:19,239] [INFO] Task started: Blastn
[2024-01-24 13:54:19,239] [INFO] Running command: blastn -query GCF_000385175.1_ASM38517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/reference_markers.fasta -out GCF_000385175.1_ASM38517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:19,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:19,896] [INFO] Selected 15 target genomes.
[2024-01-24 13:54:19,897] [INFO] Target genome list was writen to GCF_000385175.1_ASM38517v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:19,904] [INFO] Task started: fastANI
[2024-01-24 13:54:19,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fba8f7f-765f-4daa-8cf7-073a490fac33/GCF_000385175.1_ASM38517v1_genomic.fna.gz --refList GCF_000385175.1_ASM38517v1_genomic.fna/target_genomes.txt --output GCF_000385175.1_ASM38517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:27,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:27,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:27,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:27,618] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:54:27,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:27,618] [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
Salinicoccus albus	strain=YIM-Y21	GCA_000385175.1	418756	418756	type	True	100.0	860	862	95	conclusive
Salinicoccus halodurans	strain=CGMCC 1.6501	GCA_900114445.1	407035	407035	type	True	78.7552	238	862	95	below_threshold
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	78.4873	231	862	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	77.9564	144	862	95	below_threshold
Salinicoccus carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	77.8987	208	862	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	77.5734	117	862	95	below_threshold
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	76.9259	53	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:27,620] [INFO] DFAST Taxonomy check result was written to GCF_000385175.1_ASM38517v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:27,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:27,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:27,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/checkm_data
[2024-01-24 13:54:27,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:27,655] [INFO] Task started: CheckM
[2024-01-24 13:54:27,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000385175.1_ASM38517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000385175.1_ASM38517v1_genomic.fna/checkm_input GCF_000385175.1_ASM38517v1_genomic.fna/checkm_result
[2024-01-24 13:54:54,620] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:54,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:54,644] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:54,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:54,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000385175.1_ASM38517v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:54,645] [INFO] Task started: Blastn
[2024-01-24 13:54:54,645] [INFO] Running command: blastn -query GCF_000385175.1_ASM38517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0aa4102-b73e-4e32-a98c-03a8542476c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000385175.1_ASM38517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:55,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:55,467] [INFO] Selected 12 target genomes.
[2024-01-24 13:54:55,467] [INFO] Target genome list was writen to GCF_000385175.1_ASM38517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:55,478] [INFO] Task started: fastANI
[2024-01-24 13:54:55,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fba8f7f-765f-4daa-8cf7-073a490fac33/GCF_000385175.1_ASM38517v1_genomic.fna.gz --refList GCF_000385175.1_ASM38517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000385175.1_ASM38517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:02,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:02,277] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:02,277] [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_000385175.1	s__Salinicoccus albus	100.0	860	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114445.1	s__Salinicoccus halodurans	78.7552	238	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000986795.1	s__Salinicoccus sediminis	78.4873	231	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713705.1	s__Salinicoccus cyprini	77.9564	144	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000330705.1	s__Salinicoccus carnicancri	77.8987	208	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113295.1	s__Salinicoccus stercoripullorum	77.7008	199	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:02,278] [INFO] GTDB search result was written to GCF_000385175.1_ASM38517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:02,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:02,282] [INFO] DFAST_QC result json was written to GCF_000385175.1_ASM38517v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:02,282] [INFO] DFAST_QC completed!
[2024-01-24 13:55:02,282] [INFO] Total running time: 0h0m51s