[2024-01-25 18:12:05,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference
[2024-01-25 18:12:06,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,627] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg085397df-3bf8-4d39-8b3f-f9969f2cac9d/GCF_002902785.1_ASM290278v1_genomic.fna.gz | prodigal -d GCF_002902785.1_ASM290278v1_genomic.fna/cds.fna -a GCF_002902785.1_ASM290278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:11,708] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:11,709] [INFO] Task started: HMMsearch
[2024-01-25 18:12:11,709] [INFO] Running command: hmmsearch --tblout GCF_002902785.1_ASM290278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/reference_markers.hmm GCF_002902785.1_ASM290278v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:11,901] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:11,903] [INFO] Found 6/6 markers.
[2024-01-25 18:12:11,927] [INFO] Query marker FASTA was written to GCF_002902785.1_ASM290278v1_genomic.fna/markers.fasta
[2024-01-25 18:12:11,927] [INFO] Task started: Blastn
[2024-01-25 18:12:11,927] [INFO] Running command: blastn -query GCF_002902785.1_ASM290278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/reference_markers.fasta -out GCF_002902785.1_ASM290278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:12,485] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:12,487] [INFO] Selected 12 target genomes.
[2024-01-25 18:12:12,487] [INFO] Target genome list was writen to GCF_002902785.1_ASM290278v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:12,495] [INFO] Task started: fastANI
[2024-01-25 18:12:12,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg085397df-3bf8-4d39-8b3f-f9969f2cac9d/GCF_002902785.1_ASM290278v1_genomic.fna.gz --refList GCF_002902785.1_ASM290278v1_genomic.fna/target_genomes.txt --output GCF_002902785.1_ASM290278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:20,334] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:20,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:20,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:20,341] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:12:20,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:20,342] [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 delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	100.0	832	842	95	conclusive
Staphylococcus delphini	strain=NCTC12225	GCA_900636325.1	53344	53344	type	True	99.9859	840	842	95	conclusive
Staphylococcus delphini	strain=Heidy	GCA_003585325.1	53344	53344	type	True	99.9631	823	842	95	conclusive
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	93.228	692	842	95	below_threshold
Staphylococcus pseudintermedius	strain=FDAARGOS_930	GCA_016026635.1	283734	283734	type	True	93.1597	709	842	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	88.5509	686	842	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	88.5272	650	842	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	79.9399	416	842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:20,345] [INFO] DFAST Taxonomy check result was written to GCF_002902785.1_ASM290278v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:20,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:20,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:20,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/checkm_data
[2024-01-25 18:12:20,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:20,381] [INFO] Task started: CheckM
[2024-01-25 18:12:20,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902785.1_ASM290278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902785.1_ASM290278v1_genomic.fna/checkm_input GCF_002902785.1_ASM290278v1_genomic.fna/checkm_result
[2024-01-25 18:12:41,859] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:41,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:41,879] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:41,880] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:41,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902785.1_ASM290278v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:41,880] [INFO] Task started: Blastn
[2024-01-25 18:12:41,880] [INFO] Running command: blastn -query GCF_002902785.1_ASM290278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d19ac7f-6cf2-4936-94ec-a8e5eda60e91/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902785.1_ASM290278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:42,646] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:42,648] [INFO] Selected 5 target genomes.
[2024-01-25 18:12:42,648] [INFO] Target genome list was writen to GCF_002902785.1_ASM290278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:42,658] [INFO] Task started: fastANI
[2024-01-25 18:12:42,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg085397df-3bf8-4d39-8b3f-f9969f2cac9d/GCF_002902785.1_ASM290278v1_genomic.fna.gz --refList GCF_002902785.1_ASM290278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902785.1_ASM290278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:47,006] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:47,010] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:47,011] [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_900636325.1	s__Staphylococcus delphini	99.9859	840	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	conclusive
GCF_001792775.2	s__Staphylococcus pseudintermedius	93.228	692	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_010365305.1	s__Staphylococcus sp010365305	92.4298	717	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902385.1	s__Staphylococcus intermedius	88.5367	687	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_900183575.1	s__Staphylococcus cornubiensis	87.7569	706	842	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:47,012] [INFO] GTDB search result was written to GCF_002902785.1_ASM290278v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:47,013] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:47,015] [INFO] DFAST_QC result json was written to GCF_002902785.1_ASM290278v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:47,015] [INFO] DFAST_QC completed!
[2024-01-25 18:12:47,015] [INFO] Total running time: 0h0m42s