[2024-01-24 12:53:51,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:51,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:51,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference
[2024-01-24 12:53:53,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:53,064] [INFO] Task started: Prodigal
[2024-01-24 12:53:53,064] [INFO] Running command: gunzip -c /var/lib/cwl/stgf16fcabc-a069-4b64-acab-56e16ad165d4/GCF_002902745.1_ASM290274v1_genomic.fna.gz | prodigal -d GCF_002902745.1_ASM290274v1_genomic.fna/cds.fna -a GCF_002902745.1_ASM290274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:57,493] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:57,493] [INFO] Task started: HMMsearch
[2024-01-24 12:53:57,493] [INFO] Running command: hmmsearch --tblout GCF_002902745.1_ASM290274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/reference_markers.hmm GCF_002902745.1_ASM290274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:57,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:57,815] [INFO] Found 6/6 markers.
[2024-01-24 12:53:57,843] [INFO] Query marker FASTA was written to GCF_002902745.1_ASM290274v1_genomic.fna/markers.fasta
[2024-01-24 12:53:57,844] [INFO] Task started: Blastn
[2024-01-24 12:53:57,844] [INFO] Running command: blastn -query GCF_002902745.1_ASM290274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/reference_markers.fasta -out GCF_002902745.1_ASM290274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:58,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:58,460] [INFO] Selected 12 target genomes.
[2024-01-24 12:53:58,460] [INFO] Target genome list was writen to GCF_002902745.1_ASM290274v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:58,520] [INFO] Task started: fastANI
[2024-01-24 12:53:58,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgf16fcabc-a069-4b64-acab-56e16ad165d4/GCF_002902745.1_ASM290274v1_genomic.fna.gz --refList GCF_002902745.1_ASM290274v1_genomic.fna/target_genomes.txt --output GCF_002902745.1_ASM290274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:03,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:03,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:03,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:03,977] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:03,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:03,977] [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 nepalensis	strain=DSM 15150	GCA_002902745.1	214473	214473	type	True	100.0	764	781	95	conclusive
Staphylococcus nepalensis	strain=NCTC13834	GCA_900458695.1	214473	214473	type	True	99.9909	779	781	95	conclusive
Staphylococcus nepalensis	strain=CCM 7045	GCA_014635045.1	214473	214473	type	True	99.9828	777	781	95	conclusive
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	83.4826	616	781	95	below_threshold
Staphylococcus cohnii	strain=NCTC11041	GCA_900458255.1	29382	29382	type	True	83.425	585	781	95	below_threshold
Staphylococcus cohnii subsp. cohnii	strain=NCTC 11041	GCA_002902365.1	74704	29382	suspected-type	True	83.3946	589	781	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	83.1576	582	781	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.9686	464	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:03,979] [INFO] DFAST Taxonomy check result was written to GCF_002902745.1_ASM290274v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:03,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:03,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:03,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/checkm_data
[2024-01-24 12:54:03,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:04,025] [INFO] Task started: CheckM
[2024-01-24 12:54:04,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902745.1_ASM290274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902745.1_ASM290274v1_genomic.fna/checkm_input GCF_002902745.1_ASM290274v1_genomic.fna/checkm_result
[2024-01-24 12:54:25,372] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:25,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,406] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:25,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:25,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902745.1_ASM290274v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:25,407] [INFO] Task started: Blastn
[2024-01-24 12:54:25,407] [INFO] Running command: blastn -query GCF_002902745.1_ASM290274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f053c33-3a7d-4a64-97f8-f661194033da/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902745.1_ASM290274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:26,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:26,350] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:26,351] [INFO] Target genome list was writen to GCF_002902745.1_ASM290274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:26,361] [INFO] Task started: fastANI
[2024-01-24 12:54:26,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgf16fcabc-a069-4b64-acab-56e16ad165d4/GCF_002902745.1_ASM290274v1_genomic.fna.gz --refList GCF_002902745.1_ASM290274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902745.1_ASM290274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:34,039] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:34,052] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:34,053] [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_014635045.1	s__Staphylococcus nepalensis	99.9828	777	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	conclusive
GCF_002902365.1	s__Staphylococcus cohnii	83.3946	589	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_002902235.1	s__Staphylococcus ureilyticus	83.1468	583	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_016774515.1	s__Staphylococcus xylosus_A	81.0243	476	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.2953	460	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_900458565.1	s__Staphylococcus equorum	80.2915	479	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	80.2685	466	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_001006765.1	s__Staphylococcus succinus	80.2352	414	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_002732165.1	s__Staphylococcus xylosus	80.1969	450	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_000338275.1	s__Staphylococcus xylosus_B	80.1802	486	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.143	441	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431205.1	s__Staphylococcus sp001431205	79.9987	469	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900097965.1	s__Staphylococcus caeli	79.8713	408	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004785665.1	s__Staphylococcus pragensis	78.4996	211	781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:34,054] [INFO] GTDB search result was written to GCF_002902745.1_ASM290274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:34,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:34,058] [INFO] DFAST_QC result json was written to GCF_002902745.1_ASM290274v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:34,059] [INFO] DFAST_QC completed!
[2024-01-24 12:54:34,059] [INFO] Total running time: 0h0m42s