[2024-01-25 20:22:50,867] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,870] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,870] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference
[2024-01-25 20:22:52,092] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:52,092] [INFO] Task started: Prodigal
[2024-01-25 20:22:52,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgec5b3926-c216-46b2-9771-871ef09acaa3/GCF_002902385.1_ASM290238v1_genomic.fna.gz | prodigal -d GCF_002902385.1_ASM290238v1_genomic.fna/cds.fna -a GCF_002902385.1_ASM290238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:57,305] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:57,305] [INFO] Task started: HMMsearch
[2024-01-25 20:22:57,305] [INFO] Running command: hmmsearch --tblout GCF_002902385.1_ASM290238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/reference_markers.hmm GCF_002902385.1_ASM290238v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:57,548] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:57,549] [INFO] Found 6/6 markers.
[2024-01-25 20:22:57,572] [INFO] Query marker FASTA was written to GCF_002902385.1_ASM290238v1_genomic.fna/markers.fasta
[2024-01-25 20:22:57,573] [INFO] Task started: Blastn
[2024-01-25 20:22:57,573] [INFO] Running command: blastn -query GCF_002902385.1_ASM290238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/reference_markers.fasta -out GCF_002902385.1_ASM290238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:58,141] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:58,144] [INFO] Selected 12 target genomes.
[2024-01-25 20:22:58,144] [INFO] Target genome list was writen to GCF_002902385.1_ASM290238v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:58,185] [INFO] Task started: fastANI
[2024-01-25 20:22:58,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5b3926-c216-46b2-9771-871ef09acaa3/GCF_002902385.1_ASM290238v1_genomic.fna.gz --refList GCF_002902385.1_ASM290238v1_genomic.fna/target_genomes.txt --output GCF_002902385.1_ASM290238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:06,318] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:06,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:06,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:06,325] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:23:06,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:06,326] [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 intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	100.0	863	866	95	conclusive
Staphylococcus intermedius	strain=NCTC 11048	GCA_900458545.1	1285	1285	type	True	99.9944	866	866	95	conclusive
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	99.848	768	866	95	conclusive
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	89.4608	725	866	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	88.4716	678	866	95	below_threshold
Staphylococcus delphini	strain=NCTC12225	GCA_900636325.1	53344	53344	type	True	88.4304	698	866	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	88.0088	668	866	95	below_threshold
Staphylococcus pseudintermedius	strain=FDAARGOS_930	GCA_016026635.1	283734	283734	type	True	87.9393	689	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:06,327] [INFO] DFAST Taxonomy check result was written to GCF_002902385.1_ASM290238v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:06,328] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:06,328] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:06,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/checkm_data
[2024-01-25 20:23:06,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:06,358] [INFO] Task started: CheckM
[2024-01-25 20:23:06,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902385.1_ASM290238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902385.1_ASM290238v1_genomic.fna/checkm_input GCF_002902385.1_ASM290238v1_genomic.fna/checkm_result
[2024-01-25 20:23:27,646] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:27,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:27,662] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:27,662] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:27,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902385.1_ASM290238v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:27,663] [INFO] Task started: Blastn
[2024-01-25 20:23:27,663] [INFO] Running command: blastn -query GCF_002902385.1_ASM290238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0d708a7-2e57-4e34-8ae8-e5aa79a18703/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902385.1_ASM290238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:28,448] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:28,451] [INFO] Selected 5 target genomes.
[2024-01-25 20:23:28,451] [INFO] Target genome list was writen to GCF_002902385.1_ASM290238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:28,459] [INFO] Task started: fastANI
[2024-01-25 20:23:28,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5b3926-c216-46b2-9771-871ef09acaa3/GCF_002902385.1_ASM290238v1_genomic.fna.gz --refList GCF_002902385.1_ASM290238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902385.1_ASM290238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:32,452] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:32,456] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:32,457] [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_002902385.1	s__Staphylococcus intermedius	100.0	863	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	conclusive
GCF_900183575.1	s__Staphylococcus cornubiensis	89.4572	724	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365305.1	s__Staphylococcus sp010365305	88.7968	714	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636325.1	s__Staphylococcus delphini	88.4137	699	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	88.0088	668	866	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:32,458] [INFO] GTDB search result was written to GCF_002902385.1_ASM290238v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:32,458] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:32,462] [INFO] DFAST_QC result json was written to GCF_002902385.1_ASM290238v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:32,462] [INFO] DFAST_QC completed!
[2024-01-25 20:23:32,462] [INFO] Total running time: 0h0m42s