[2024-01-24 13:57:30,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:30,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:30,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference
[2024-01-24 13:57:31,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:31,987] [INFO] Task started: Prodigal
[2024-01-24 13:57:31,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f58466f-36f6-4ce0-a834-db4c89bbbf3c/GCF_002902285.1_ASM290228v1_genomic.fna.gz | prodigal -d GCF_002902285.1_ASM290228v1_genomic.fna/cds.fna -a GCF_002902285.1_ASM290228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:37,197] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:37,198] [INFO] Task started: HMMsearch
[2024-01-24 13:57:37,198] [INFO] Running command: hmmsearch --tblout GCF_002902285.1_ASM290228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/reference_markers.hmm GCF_002902285.1_ASM290228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:37,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:37,444] [INFO] Found 6/6 markers.
[2024-01-24 13:57:37,473] [INFO] Query marker FASTA was written to GCF_002902285.1_ASM290228v1_genomic.fna/markers.fasta
[2024-01-24 13:57:37,474] [INFO] Task started: Blastn
[2024-01-24 13:57:37,474] [INFO] Running command: blastn -query GCF_002902285.1_ASM290228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/reference_markers.fasta -out GCF_002902285.1_ASM290228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:38,077] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:38,080] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:38,081] [INFO] Target genome list was writen to GCF_002902285.1_ASM290228v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:38,089] [INFO] Task started: fastANI
[2024-01-24 13:57:38,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f58466f-36f6-4ce0-a834-db4c89bbbf3c/GCF_002902285.1_ASM290228v1_genomic.fna.gz --refList GCF_002902285.1_ASM290228v1_genomic.fna/target_genomes.txt --output GCF_002902285.1_ASM290228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:45,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:45,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:45,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:45,382] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:45,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:45,383] [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
Staphylococcus simulans	strain=NCTC 11046	GCA_002902285.1	1286	1286	type	True	100.0	877	879	95	conclusive
Staphylococcus simulans	strain=NCTC11046	GCA_900474685.1	1286	1286	type	True	99.9923	876	879	95	conclusive
Staphylococcus condimenti	strain=DSM 11674	GCA_001618885.1	70255	70255	type	True	81.108	501	879	95	below_threshold
Staphylococcus condimenti	strain=NCTC13827	GCA_900637235.1	70255	70255	type	True	81.106	514	879	95	below_threshold
Staphylococcus condimenti	strain=DSM 11674	GCA_001014685.1	70255	70255	type	True	81.0444	504	879	95	below_threshold
Staphylococcus carnosus	strain=NCTC13825	GCA_900458435.1	1281	1281	type	True	81.0037	516	879	95	below_threshold
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	80.9796	528	879	95	below_threshold
Staphylococcus piscifermentans	strain=DSM 7373	GCA_003970555.1	70258	70258	type	True	80.549	486	879	95	below_threshold
Staphylococcus piscifermentans	strain=NCTC13836	GCA_900186985.1	70258	70258	type	True	80.5371	498	879	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.194	205	879	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	77.9653	73	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,385] [INFO] DFAST Taxonomy check result was written to GCF_002902285.1_ASM290228v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:45,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:45,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:45,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/checkm_data
[2024-01-24 13:57:45,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:45,420] [INFO] Task started: CheckM
[2024-01-24 13:57:45,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902285.1_ASM290228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902285.1_ASM290228v1_genomic.fna/checkm_input GCF_002902285.1_ASM290228v1_genomic.fna/checkm_result
[2024-01-24 13:58:08,444] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:08,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,468] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:08,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:08,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902285.1_ASM290228v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:08,469] [INFO] Task started: Blastn
[2024-01-24 13:58:08,470] [INFO] Running command: blastn -query GCF_002902285.1_ASM290228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64ac1de4-b6fc-45a1-b633-f0eb0c9d1e2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902285.1_ASM290228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:09,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:09,320] [INFO] Selected 8 target genomes.
[2024-01-24 13:58:09,320] [INFO] Target genome list was writen to GCF_002902285.1_ASM290228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:09,330] [INFO] Task started: fastANI
[2024-01-24 13:58:09,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f58466f-36f6-4ce0-a834-db4c89bbbf3c/GCF_002902285.1_ASM290228v1_genomic.fna.gz --refList GCF_002902285.1_ASM290228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902285.1_ASM290228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:14,355] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:14,364] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:14,364] [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_002902285.1	s__Staphylococcus simulans	100.0	877	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	conclusive
GCF_003043455.1	s__Staphylococcus simulans_A	93.4038	726	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
GCF_002994445.1	s__Staphylococcus simulans_B	83.6238	644	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	96.89	96.89	0.92	0.92	2	-
GCF_001618885.1	s__Staphylococcus condimenti	81.0823	503	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	-
GCF_900458435.1	s__Staphylococcus carnosus	81.0037	516	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCF_003718735.1	s__Staphylococcus debuckii	80.7873	487	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900186985.1	s__Staphylococcus piscifermentans	80.5249	499	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_001224225.1	s__Staphylococcus borealis	78.8457	230	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:14,366] [INFO] GTDB search result was written to GCF_002902285.1_ASM290228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:14,366] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:14,369] [INFO] DFAST_QC result json was written to GCF_002902285.1_ASM290228v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:14,370] [INFO] DFAST_QC completed!
[2024-01-24 13:58:14,370] [INFO] Total running time: 0h0m44s