[2024-01-25 18:11:50,395] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:50,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:50,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference
[2024-01-25 18:11:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:51,532] [INFO] Task started: Prodigal
[2024-01-25 18:11:51,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgd32bda1e-5fe0-439f-9a5f-991b6cb8033f/GCF_016238445.1_ASM1623844v1_genomic.fna.gz | prodigal -d GCF_016238445.1_ASM1623844v1_genomic.fna/cds.fna -a GCF_016238445.1_ASM1623844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:55,095] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:55,096] [INFO] Task started: HMMsearch
[2024-01-25 18:11:55,096] [INFO] Running command: hmmsearch --tblout GCF_016238445.1_ASM1623844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/reference_markers.hmm GCF_016238445.1_ASM1623844v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:55,288] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:55,289] [INFO] Found 6/6 markers.
[2024-01-25 18:11:55,310] [INFO] Query marker FASTA was written to GCF_016238445.1_ASM1623844v1_genomic.fna/markers.fasta
[2024-01-25 18:11:55,310] [INFO] Task started: Blastn
[2024-01-25 18:11:55,310] [INFO] Running command: blastn -query GCF_016238445.1_ASM1623844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/reference_markers.fasta -out GCF_016238445.1_ASM1623844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:55,873] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:55,876] [INFO] Selected 21 target genomes.
[2024-01-25 18:11:55,876] [INFO] Target genome list was writen to GCF_016238445.1_ASM1623844v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:55,906] [INFO] Task started: fastANI
[2024-01-25 18:11:55,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32bda1e-5fe0-439f-9a5f-991b6cb8033f/GCF_016238445.1_ASM1623844v1_genomic.fna.gz --refList GCF_016238445.1_ASM1623844v1_genomic.fna/target_genomes.txt --output GCF_016238445.1_ASM1623844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:04,768] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:04,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:04,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:04,779] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:04,779] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:04,779] [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 canis	strain=H16/1A	GCA_016238445.1	2724942	2724942	type	True	100.0	705	707	95	conclusive
Staphylococcus felis	strain=FDAARGOS_1014	GCA_016127055.1	46127	46127	type	True	80.4595	390	707	95	below_threshold
Staphylococcus felis	strain=DSM 7377	GCA_002902185.1	46127	46127	type	True	80.4487	367	707	95	below_threshold
Staphylococcus felis	strain=ATCC 49168	GCA_003012915.1	46127	46127	type	True	80.388	392	707	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	78.9317	253	707	95	below_threshold
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	78.8541	243	707	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	78.8357	262	707	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	78.8253	262	707	95	below_threshold
Staphylococcus schleiferi subsp. schleiferi	strain=NCTC 12218	GCA_003968865.1	74707	1295	type	True	78.6993	260	707	95	below_threshold
Staphylococcus schleiferi	strain=ATCC 43808	GCA_011137195.1	1295	1295	type	True	78.6833	256	707	95	below_threshold
Staphylococcus coagulans	strain=DSM 6628	GCA_002901995.1	74706	74706	type	True	78.6819	259	707	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	78.5375	178	707	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	78.3121	183	707	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC12103	GCA_900474615.1	1296	1296	type	True	77.9401	138	707	95	below_threshold
Mammaliicoccus sciuri	strain=NCTC 12103	GCA_002901825.1	1296	1296	type	True	77.8708	135	707	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	77.7727	136	707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:04,780] [INFO] DFAST Taxonomy check result was written to GCF_016238445.1_ASM1623844v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:04,782] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:04,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:04,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/checkm_data
[2024-01-25 18:12:04,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:04,808] [INFO] Task started: CheckM
[2024-01-25 18:12:04,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016238445.1_ASM1623844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016238445.1_ASM1623844v1_genomic.fna/checkm_input GCF_016238445.1_ASM1623844v1_genomic.fna/checkm_result
[2024-01-25 18:12:22,518] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:22,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:22,536] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:22,536] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:22,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016238445.1_ASM1623844v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:22,536] [INFO] Task started: Blastn
[2024-01-25 18:12:22,537] [INFO] Running command: blastn -query GCF_016238445.1_ASM1623844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefa5c608-8f10-4728-a207-1dba864c2baa/dqc_reference/reference_markers_gtdb.fasta -out GCF_016238445.1_ASM1623844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:23,315] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:23,319] [INFO] Selected 21 target genomes.
[2024-01-25 18:12:23,319] [INFO] Target genome list was writen to GCF_016238445.1_ASM1623844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:23,345] [INFO] Task started: fastANI
[2024-01-25 18:12:23,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgd32bda1e-5fe0-439f-9a5f-991b6cb8033f/GCF_016238445.1_ASM1623844v1_genomic.fna.gz --refList GCF_016238445.1_ASM1623844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016238445.1_ASM1623844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:33,284] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:33,300] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:33,300] [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_016238445.1	s__Staphylococcus sp016238445	100.0	705	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003012915.1	s__Staphylococcus felis	80.388	392	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.9963	268	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019255.1	s__Staphylococcus kloosii	78.9693	163	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	78.9317	253	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_013463155.1	s__Staphylococcus sp013463155	78.9308	229	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900183575.1	s__Staphylococcus cornubiensis	78.9272	277	707	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	78.8792	281	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_002901865.1	s__Staphylococcus agnetis	78.8721	242	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCA_900458895.2	s__Staphylococcus schleiferi	78.8253	262	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_900636325.1	s__Staphylococcus delphini	78.7992	263	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_002901945.1	s__Staphylococcus chromogenes	78.7135	244	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_002901995.1	s__Staphylococcus coagulans	78.6819	259	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_001027105.1	s__Staphylococcus aureus	78.6308	181	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	-
GCF_004785665.1	s__Staphylococcus pragensis	78.548	174	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.3131	177	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002902565.1	s__Staphylococcus petrasii	78.3121	183	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_002901825.1	s__Mammaliicoccus sciuri	77.8627	136	707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:33,301] [INFO] GTDB search result was written to GCF_016238445.1_ASM1623844v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:33,302] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:33,305] [INFO] DFAST_QC result json was written to GCF_016238445.1_ASM1623844v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:33,305] [INFO] DFAST_QC completed!
[2024-01-25 18:12:33,305] [INFO] Total running time: 0h0m43s