[2024-01-25 19:35:05,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference
[2024-01-25 19:35:06,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,833] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgdddc61be-9ea0-4f93-8666-4bad6a2781ea/GCF_003012915.1_ASM301291v1_genomic.fna.gz | prodigal -d GCF_003012915.1_ASM301291v1_genomic.fna/cds.fna -a GCF_003012915.1_ASM301291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:11,166] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:11,167] [INFO] Task started: HMMsearch
[2024-01-25 19:35:11,167] [INFO] Running command: hmmsearch --tblout GCF_003012915.1_ASM301291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/reference_markers.hmm GCF_003012915.1_ASM301291v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:11,432] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:11,434] [INFO] Found 6/6 markers.
[2024-01-25 19:35:11,456] [INFO] Query marker FASTA was written to GCF_003012915.1_ASM301291v1_genomic.fna/markers.fasta
[2024-01-25 19:35:11,456] [INFO] Task started: Blastn
[2024-01-25 19:35:11,456] [INFO] Running command: blastn -query GCF_003012915.1_ASM301291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/reference_markers.fasta -out GCF_003012915.1_ASM301291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:12,041] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:12,044] [INFO] Selected 15 target genomes.
[2024-01-25 19:35:12,045] [INFO] Target genome list was writen to GCF_003012915.1_ASM301291v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:12,049] [INFO] Task started: fastANI
[2024-01-25 19:35:12,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgdddc61be-9ea0-4f93-8666-4bad6a2781ea/GCF_003012915.1_ASM301291v1_genomic.fna.gz --refList GCF_003012915.1_ASM301291v1_genomic.fna/target_genomes.txt --output GCF_003012915.1_ASM301291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:22,479] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:22,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:22,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:22,488] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:35:22,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:22,488] [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 felis	strain=ATCC 49168	GCA_003012915.1	46127	46127	type	True	100.0	826	826	95	conclusive
Staphylococcus felis	strain=FDAARGOS_1014	GCA_016127055.1	46127	46127	type	True	99.9964	824	826	95	conclusive
Staphylococcus felis	strain=DSM 7377	GCA_002902185.1	46127	46127	type	True	99.8301	712	826	95	conclusive
Staphylococcus canis	strain=H16/1A	GCA_016238445.1	2724942	2724942	type	True	80.0616	415	826	95	below_threshold
Staphylococcus microti	strain=NCTC13832	GCA_900458705.1	569857	569857	type	True	79.4547	230	826	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	79.1979	291	826	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	79.195	260	826	95	below_threshold
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	78.9916	282	826	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	78.8351	229	826	95	below_threshold
Staphylococcus microti	strain=DSM 22147	GCA_000934465.1	569857	569857	type	True	78.735	215	826	95	below_threshold
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	78.5989	242	826	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	77.7705	158	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:22,490] [INFO] DFAST Taxonomy check result was written to GCF_003012915.1_ASM301291v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:22,490] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:22,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:22,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/checkm_data
[2024-01-25 19:35:22,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:22,520] [INFO] Task started: CheckM
[2024-01-25 19:35:22,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012915.1_ASM301291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012915.1_ASM301291v1_genomic.fna/checkm_input GCF_003012915.1_ASM301291v1_genomic.fna/checkm_result
[2024-01-25 19:35:41,529] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:41,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:41,544] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:41,544] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:41,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012915.1_ASM301291v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:41,545] [INFO] Task started: Blastn
[2024-01-25 19:35:41,545] [INFO] Running command: blastn -query GCF_003012915.1_ASM301291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59731bd9-7dd2-4046-b747-a232b747c06e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012915.1_ASM301291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:42,317] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:42,320] [INFO] Selected 14 target genomes.
[2024-01-25 19:35:42,320] [INFO] Target genome list was writen to GCF_003012915.1_ASM301291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:42,326] [INFO] Task started: fastANI
[2024-01-25 19:35:42,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgdddc61be-9ea0-4f93-8666-4bad6a2781ea/GCF_003012915.1_ASM301291v1_genomic.fna.gz --refList GCF_003012915.1_ASM301291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012915.1_ASM301291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:51,288] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:51,298] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:51,298] [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_003012915.1	s__Staphylococcus felis	100.0	824	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	conclusive
GCF_016238445.1	s__Staphylococcus sp016238445	80.0616	415	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101335.1	s__Staphylococcus lutrae	79.7511	241	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010365305.1	s__Staphylococcus sp010365305	79.683	268	826	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	79.2078	241	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	79.2039	260	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCA_900458895.2	s__Staphylococcus schleiferi	79.1548	291	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.0569	168	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.0092	280	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901995.1	s__Staphylococcus coagulans	78.7528	272	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_000934465.1	s__Staphylococcus microti	78.7158	216	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002901865.1	s__Staphylococcus agnetis	78.5989	242	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_900636385.1	s__Staphylococcus warneri	78.5518	169	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_002902365.1	s__Staphylococcus cohnii	77.6745	156	826	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:51,300] [INFO] GTDB search result was written to GCF_003012915.1_ASM301291v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:51,300] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:51,305] [INFO] DFAST_QC result json was written to GCF_003012915.1_ASM301291v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:51,305] [INFO] DFAST_QC completed!
[2024-01-25 19:35:51,306] [INFO] Total running time: 0h0m46s