[2024-01-24 13:25:31,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,330] [INFO] DQC Reference Directory: /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference
[2024-01-24 13:25:32,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,685] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,685] [INFO] Running command: gunzip -c /var/lib/cwl/stge31cc9f1-40ec-4db5-9daf-1d7bd8749311/GCF_002087975.1_ASM208797v1_genomic.fna.gz | prodigal -d GCF_002087975.1_ASM208797v1_genomic.fna/cds.fna -a GCF_002087975.1_ASM208797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:37,125] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:37,125] [INFO] Task started: HMMsearch
[2024-01-24 13:25:37,126] [INFO] Running command: hmmsearch --tblout GCF_002087975.1_ASM208797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/reference_markers.hmm GCF_002087975.1_ASM208797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:37,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:37,374] [INFO] Found 6/6 markers.
[2024-01-24 13:25:37,402] [INFO] Query marker FASTA was written to GCF_002087975.1_ASM208797v1_genomic.fna/markers.fasta
[2024-01-24 13:25:37,402] [INFO] Task started: Blastn
[2024-01-24 13:25:37,402] [INFO] Running command: blastn -query GCF_002087975.1_ASM208797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/reference_markers.fasta -out GCF_002087975.1_ASM208797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:38,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:38,029] [INFO] Selected 10 target genomes.
[2024-01-24 13:25:38,029] [INFO] Target genome list was writen to GCF_002087975.1_ASM208797v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:38,038] [INFO] Task started: fastANI
[2024-01-24 13:25:38,038] [INFO] Running command: fastANI --query /var/lib/cwl/stge31cc9f1-40ec-4db5-9daf-1d7bd8749311/GCF_002087975.1_ASM208797v1_genomic.fna.gz --refList GCF_002087975.1_ASM208797v1_genomic.fna/target_genomes.txt --output GCF_002087975.1_ASM208797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:44,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:44,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:44,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:44,679] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:25:44,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:44,679] [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 epidermidis	strain=ATCC 14990	GCA_002087975.1	1282	1282	type	True	100.0	801	802	95	conclusive
Staphylococcus epidermidis	strain=NBRC 100911	GCA_006742205.1	1282	1282	type	True	99.9931	782	802	95	conclusive
Staphylococcus epidermidis	strain=NCTC11047	GCA_900458605.1	1282	1282	type	True	99.9927	798	802	95	conclusive
Staphylococcus epidermidis	strain=ATCC 14990	GCA_006094375.1	1282	1282	type	True	99.9892	800	802	95	conclusive
Staphylococcus epidermidis	strain=NCTC 11047	GCA_002901875.1	1282	1282	type	True	99.9736	779	802	95	conclusive
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.51	332	802	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.8417	318	802	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.7846	324	802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:44,681] [INFO] DFAST Taxonomy check result was written to GCF_002087975.1_ASM208797v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:44,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:44,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:44,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/checkm_data
[2024-01-24 13:25:44,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:44,709] [INFO] Task started: CheckM
[2024-01-24 13:25:44,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002087975.1_ASM208797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002087975.1_ASM208797v1_genomic.fna/checkm_input GCF_002087975.1_ASM208797v1_genomic.fna/checkm_result
[2024-01-24 13:26:05,765] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:05,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:05,785] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:05,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:05,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002087975.1_ASM208797v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:05,787] [INFO] Task started: Blastn
[2024-01-24 13:26:05,787] [INFO] Running command: blastn -query GCF_002087975.1_ASM208797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc129b1f4-48a4-44d1-915e-7d361eb2247e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002087975.1_ASM208797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:06,603] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:06,607] [INFO] Selected 15 target genomes.
[2024-01-24 13:26:06,607] [INFO] Target genome list was writen to GCF_002087975.1_ASM208797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:06,622] [INFO] Task started: fastANI
[2024-01-24 13:26:06,622] [INFO] Running command: fastANI --query /var/lib/cwl/stge31cc9f1-40ec-4db5-9daf-1d7bd8749311/GCF_002087975.1_ASM208797v1_genomic.fna.gz --refList GCF_002087975.1_ASM208797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002087975.1_ASM208797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:14,544] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:14,561] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:14,562] [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_006742205.1	s__Staphylococcus epidermidis	99.9688	783	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.01	96.59	0.94	0.83	1079	conclusive
GCF_900458815.1	s__Staphylococcus saccharolyticus	81.5108	521	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	-
GCF_002902325.1	s__Staphylococcus capitis	80.7931	482	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_002902725.1	s__Staphylococcus caprae	80.6693	479	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_001224225.1	s__Staphylococcus borealis	79.8368	330	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_004785665.1	s__Staphylococcus pragensis	79.8284	327	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCA_002902575.1	s__Staphylococcus croceilyticus	79.7385	308	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_900636385.1	s__Staphylococcus warneri	79.6286	380	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.5835	368	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_006094395.1	s__Staphylococcus haemolyticus	79.4599	359	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_002902565.1	s__Staphylococcus petrasii	79.453	322	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_003035445.1	s__Staphylococcus devriesei_A	79.4041	311	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_002902625.1	s__Staphylococcus devriesei	79.2014	291	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_002902085.1	s__Staphylococcus simiae	78.5823	326	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_003043455.1	s__Staphylococcus simulans_A	78.3927	172	802	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:14,563] [INFO] GTDB search result was written to GCF_002087975.1_ASM208797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:14,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:14,567] [INFO] DFAST_QC result json was written to GCF_002087975.1_ASM208797v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:14,568] [INFO] DFAST_QC completed!
[2024-01-24 13:26:14,568] [INFO] Total running time: 0h0m43s