[2024-01-24 13:55:48,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:48,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:48,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference
[2024-01-24 13:55:49,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,599] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfa45ca2-01fc-4608-a1c9-bee8177cfa99/GCF_000308095.1_ASM30809v1_genomic.fna.gz | prodigal -d GCF_000308095.1_ASM30809v1_genomic.fna/cds.fna -a GCF_000308095.1_ASM30809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:55,276] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:55,277] [INFO] Task started: HMMsearch
[2024-01-24 13:55:55,277] [INFO] Running command: hmmsearch --tblout GCF_000308095.1_ASM30809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/reference_markers.hmm GCF_000308095.1_ASM30809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:55,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:55,538] [INFO] Found 6/6 markers.
[2024-01-24 13:55:55,566] [INFO] Query marker FASTA was written to GCF_000308095.1_ASM30809v1_genomic.fna/markers.fasta
[2024-01-24 13:55:55,566] [INFO] Task started: Blastn
[2024-01-24 13:55:55,566] [INFO] Running command: blastn -query GCF_000308095.1_ASM30809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/reference_markers.fasta -out GCF_000308095.1_ASM30809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:56,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:56,162] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:56,162] [INFO] Target genome list was writen to GCF_000308095.1_ASM30809v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:56,189] [INFO] Task started: fastANI
[2024-01-24 13:55:56,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa45ca2-01fc-4608-a1c9-bee8177cfa99/GCF_000308095.1_ASM30809v1_genomic.fna.gz --refList GCF_000308095.1_ASM30809v1_genomic.fna/target_genomes.txt --output GCF_000308095.1_ASM30809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:03,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:03,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:03,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:03,514] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:03,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:03,514] [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_000308095.1	1285	1285	type	True	100.0	789	796	95	conclusive
Staphylococcus intermedius	strain=NCTC 11048	GCA_900458545.1	1285	1285	type	True	99.9905	796	796	95	conclusive
Staphylococcus intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	99.917	778	796	95	conclusive
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	89.546	678	796	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	88.5739	635	796	95	below_threshold
Staphylococcus delphini	strain=NCTC12225	GCA_900636325.1	53344	53344	type	True	88.5404	666	796	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	88.213	628	796	95	below_threshold
Staphylococcus pseudintermedius	strain=FDAARGOS_930	GCA_016026635.1	283734	283734	type	True	88.1432	647	796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:03,516] [INFO] DFAST Taxonomy check result was written to GCF_000308095.1_ASM30809v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:03,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:03,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:03,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/checkm_data
[2024-01-24 13:56:03,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:03,546] [INFO] Task started: CheckM
[2024-01-24 13:56:03,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308095.1_ASM30809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308095.1_ASM30809v1_genomic.fna/checkm_input GCF_000308095.1_ASM30809v1_genomic.fna/checkm_result
[2024-01-24 13:56:27,659] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:27,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:27,680] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:27,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:27,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308095.1_ASM30809v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:27,681] [INFO] Task started: Blastn
[2024-01-24 13:56:27,682] [INFO] Running command: blastn -query GCF_000308095.1_ASM30809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18a38469-7b32-43b6-8e6c-f0c0f84becb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308095.1_ASM30809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:28,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:28,457] [INFO] Selected 5 target genomes.
[2024-01-24 13:56:28,457] [INFO] Target genome list was writen to GCF_000308095.1_ASM30809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:28,473] [INFO] Task started: fastANI
[2024-01-24 13:56:28,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa45ca2-01fc-4608-a1c9-bee8177cfa99/GCF_000308095.1_ASM30809v1_genomic.fna.gz --refList GCF_000308095.1_ASM30809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308095.1_ASM30809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:32,037] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:32,047] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:32,048] [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	99.917	778	796	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	89.546	678	796	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	89.0352	667	796	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	88.5617	665	796	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	88.1835	631	796	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:32,049] [INFO] GTDB search result was written to GCF_000308095.1_ASM30809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:32,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:32,052] [INFO] DFAST_QC result json was written to GCF_000308095.1_ASM30809v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:32,053] [INFO] DFAST_QC completed!
[2024-01-24 13:56:32,053] [INFO] Total running time: 0h0m44s