[2024-01-25 20:19:20,696] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference
[2024-01-25 20:19:21,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,861] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg80499605-d2ad-4f14-a426-9786a9e30b84/GCF_016724565.1_ASM1672456v1_genomic.fna.gz | prodigal -d GCF_016724565.1_ASM1672456v1_genomic.fna/cds.fna -a GCF_016724565.1_ASM1672456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:26,587] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:26,587] [INFO] Task started: HMMsearch
[2024-01-25 20:19:26,587] [INFO] Running command: hmmsearch --tblout GCF_016724565.1_ASM1672456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/reference_markers.hmm GCF_016724565.1_ASM1672456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:26,824] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:26,825] [INFO] Found 6/6 markers.
[2024-01-25 20:19:26,861] [INFO] Query marker FASTA was written to GCF_016724565.1_ASM1672456v1_genomic.fna/markers.fasta
[2024-01-25 20:19:26,861] [INFO] Task started: Blastn
[2024-01-25 20:19:26,861] [INFO] Running command: blastn -query GCF_016724565.1_ASM1672456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/reference_markers.fasta -out GCF_016724565.1_ASM1672456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:27,443] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:27,445] [INFO] Selected 10 target genomes.
[2024-01-25 20:19:27,446] [INFO] Target genome list was writen to GCF_016724565.1_ASM1672456v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:27,449] [INFO] Task started: fastANI
[2024-01-25 20:19:27,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg80499605-d2ad-4f14-a426-9786a9e30b84/GCF_016724565.1_ASM1672456v1_genomic.fna.gz --refList GCF_016724565.1_ASM1672456v1_genomic.fna/target_genomes.txt --output GCF_016724565.1_ASM1672456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:32,946] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:32,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:32,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:32,953] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 20:19:32,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:32,953] [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 condimenti	strain=FDAARGOS_1148	GCA_016724565.1	70255	70255	type	True	100.0	886	886	95	conclusive
Staphylococcus condimenti	strain=NCTC13827	GCA_900637235.1	70255	70255	type	True	100.0	882	886	95	conclusive
Staphylococcus condimenti	strain=DSM 11674	GCA_001618885.1	70255	70255	type	True	99.9987	883	886	95	conclusive
Staphylococcus condimenti	strain=DSM 11674	GCA_001014685.1	70255	70255	type	True	99.9669	848	886	95	conclusive
Staphylococcus condimenti	strain=DSM 11674	GCA_002902505.1	70255	70255	type	True	99.8695	783	886	95	conclusive
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.6117	235	886	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.0037	229	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:32,955] [INFO] DFAST Taxonomy check result was written to GCF_016724565.1_ASM1672456v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:32,956] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:32,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:32,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/checkm_data
[2024-01-25 20:19:32,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:32,983] [INFO] Task started: CheckM
[2024-01-25 20:19:32,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016724565.1_ASM1672456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016724565.1_ASM1672456v1_genomic.fna/checkm_input GCF_016724565.1_ASM1672456v1_genomic.fna/checkm_result
[2024-01-25 20:19:53,282] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:53,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:53,306] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:53,306] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:53,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016724565.1_ASM1672456v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:53,307] [INFO] Task started: Blastn
[2024-01-25 20:19:53,307] [INFO] Running command: blastn -query GCF_016724565.1_ASM1672456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80ccc5f-9ce6-4a67-b456-a6b71d3a0e2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016724565.1_ASM1672456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:54,082] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:54,084] [INFO] Selected 7 target genomes.
[2024-01-25 20:19:54,084] [INFO] Target genome list was writen to GCF_016724565.1_ASM1672456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:54,089] [INFO] Task started: fastANI
[2024-01-25 20:19:54,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg80499605-d2ad-4f14-a426-9786a9e30b84/GCF_016724565.1_ASM1672456v1_genomic.fna.gz --refList GCF_016724565.1_ASM1672456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016724565.1_ASM1672456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:58,829] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:58,834] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:58,835] [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_001618885.1	s__Staphylococcus condimenti	99.9987	883	886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	conclusive
GCF_900458435.1	s__Staphylococcus carnosus	91.9347	781	886	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	85.1059	723	886	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	85.0122	720	886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_002902285.1	s__Staphylococcus simulans	81.1963	503	886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_003043455.1	s__Staphylococcus simulans_A	81.194	476	886	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	80.7506	511	886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	96.89	96.89	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:58,836] [INFO] GTDB search result was written to GCF_016724565.1_ASM1672456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:58,836] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:58,839] [INFO] DFAST_QC result json was written to GCF_016724565.1_ASM1672456v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:58,839] [INFO] DFAST_QC completed!
[2024-01-25 20:19:58,839] [INFO] Total running time: 0h0m38s