[2024-01-25 19:55:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:35,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:35,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference
[2024-01-25 19:55:36,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:36,629] [INFO] Task started: Prodigal
[2024-01-25 19:55:36,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c985e18-d5ab-43d4-b51e-b13bbd63ec7c/GCF_002901875.1_ASM290187v1_genomic.fna.gz | prodigal -d GCF_002901875.1_ASM290187v1_genomic.fna/cds.fna -a GCF_002901875.1_ASM290187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:40,373] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:40,373] [INFO] Task started: HMMsearch
[2024-01-25 19:55:40,373] [INFO] Running command: hmmsearch --tblout GCF_002901875.1_ASM290187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/reference_markers.hmm GCF_002901875.1_ASM290187v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:40,585] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:40,587] [INFO] Found 6/6 markers.
[2024-01-25 19:55:40,607] [INFO] Query marker FASTA was written to GCF_002901875.1_ASM290187v1_genomic.fna/markers.fasta
[2024-01-25 19:55:40,607] [INFO] Task started: Blastn
[2024-01-25 19:55:40,607] [INFO] Running command: blastn -query GCF_002901875.1_ASM290187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/reference_markers.fasta -out GCF_002901875.1_ASM290187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:41,199] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:41,202] [INFO] Selected 10 target genomes.
[2024-01-25 19:55:41,202] [INFO] Target genome list was writen to GCF_002901875.1_ASM290187v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:41,214] [INFO] Task started: fastANI
[2024-01-25 19:55:41,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c985e18-d5ab-43d4-b51e-b13bbd63ec7c/GCF_002901875.1_ASM290187v1_genomic.fna.gz --refList GCF_002901875.1_ASM290187v1_genomic.fna/target_genomes.txt --output GCF_002901875.1_ASM290187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:48,089] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:48,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:48,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:48,096] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:55:48,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:48,096] [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=NCTC 11047	GCA_002901875.1	1282	1282	type	True	100.0	788	792	95	conclusive
Staphylococcus epidermidis	strain=ATCC 14990	GCA_002087975.1	1282	1282	type	True	99.9855	789	792	95	conclusive
Staphylococcus epidermidis	strain=ATCC 14990	GCA_006094375.1	1282	1282	type	True	99.9848	789	792	95	conclusive
Staphylococcus epidermidis	strain=NCTC11047	GCA_900458605.1	1282	1282	type	True	99.983	788	792	95	conclusive
Staphylococcus epidermidis	strain=NBRC 100911	GCA_006742205.1	1282	1282	type	True	99.9674	774	792	95	conclusive
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.3673	325	792	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.7688	316	792	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.6591	308	792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:48,098] [INFO] DFAST Taxonomy check result was written to GCF_002901875.1_ASM290187v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:48,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:48,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:48,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/checkm_data
[2024-01-25 19:55:48,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:48,134] [INFO] Task started: CheckM
[2024-01-25 19:55:48,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901875.1_ASM290187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901875.1_ASM290187v1_genomic.fna/checkm_input GCF_002901875.1_ASM290187v1_genomic.fna/checkm_result
[2024-01-25 19:56:06,169] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:06,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:06,192] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:06,192] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:06,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901875.1_ASM290187v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:06,193] [INFO] Task started: Blastn
[2024-01-25 19:56:06,193] [INFO] Running command: blastn -query GCF_002901875.1_ASM290187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6c6150-ca98-45d1-be2d-07e79f2d806f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901875.1_ASM290187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:06,994] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:06,997] [INFO] Selected 15 target genomes.
[2024-01-25 19:56:06,997] [INFO] Target genome list was writen to GCF_002901875.1_ASM290187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:07,008] [INFO] Task started: fastANI
[2024-01-25 19:56:07,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c985e18-d5ab-43d4-b51e-b13bbd63ec7c/GCF_002901875.1_ASM290187v1_genomic.fna.gz --refList GCF_002901875.1_ASM290187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901875.1_ASM290187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:14,791] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:14,801] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:14,801] [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	99.9674	774	792	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	81.3966	527	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.11	97.94	0.98	0.95	15	-
GCF_002902725.1	s__Staphylococcus caprae	80.8215	469	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_002902325.1	s__Staphylococcus capitis	80.6229	491	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_001224225.1	s__Staphylococcus borealis	79.8085	327	792	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	79.6216	315	792	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	79.5559	320	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_006094395.1	s__Staphylococcus haemolyticus	79.5068	354	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_900636385.1	s__Staphylococcus warneri	79.4678	381	792	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	79.3922	364	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902565.1	s__Staphylococcus petrasii	79.3707	324	792	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	79.3428	313	792	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	79.2856	285	792	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	78.6532	318	792	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	78.0903	174	792	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:14,803] [INFO] GTDB search result was written to GCF_002901875.1_ASM290187v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:14,803] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:14,806] [INFO] DFAST_QC result json was written to GCF_002901875.1_ASM290187v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:14,806] [INFO] DFAST_QC completed!
[2024-01-25 19:56:14,806] [INFO] Total running time: 0h0m39s