[2024-01-24 11:05:28,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,093] [INFO] DQC Reference Directory: /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference
[2024-01-24 11:05:29,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,410] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,410] [INFO] Running command: gunzip -c /var/lib/cwl/stge2146735-13bf-4ffc-b8a7-362231f4d49f/GCF_900474685.1_40961_B01_genomic.fna.gz | prodigal -d GCF_900474685.1_40961_B01_genomic.fna/cds.fna -a GCF_900474685.1_40961_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:35,259] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:35,259] [INFO] Task started: HMMsearch
[2024-01-24 11:05:35,259] [INFO] Running command: hmmsearch --tblout GCF_900474685.1_40961_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/reference_markers.hmm GCF_900474685.1_40961_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:35,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:35,565] [INFO] Found 6/6 markers.
[2024-01-24 11:05:35,611] [INFO] Query marker FASTA was written to GCF_900474685.1_40961_B01_genomic.fna/markers.fasta
[2024-01-24 11:05:35,611] [INFO] Task started: Blastn
[2024-01-24 11:05:35,611] [INFO] Running command: blastn -query GCF_900474685.1_40961_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/reference_markers.fasta -out GCF_900474685.1_40961_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:36,308] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:36,312] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:36,313] [INFO] Target genome list was writen to GCF_900474685.1_40961_B01_genomic.fna/target_genomes.txt
[2024-01-24 11:05:36,325] [INFO] Task started: fastANI
[2024-01-24 11:05:36,325] [INFO] Running command: fastANI --query /var/lib/cwl/stge2146735-13bf-4ffc-b8a7-362231f4d49f/GCF_900474685.1_40961_B01_genomic.fna.gz --refList GCF_900474685.1_40961_B01_genomic.fna/target_genomes.txt --output GCF_900474685.1_40961_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:44,039] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:44,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:44,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:44,051] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:44,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:44,051] [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 simulans	strain=NCTC11046	GCA_900474685.1	1286	1286	type	True	100.0	920	920	95	conclusive
Staphylococcus simulans	strain=NCTC 11046	GCA_002902285.1	1286	1286	type	True	99.9292	868	920	95	conclusive
Staphylococcus condimenti	strain=DSM 11674	GCA_001618885.1	70255	70255	type	True	81.6746	499	920	95	below_threshold
Staphylococcus condimenti	strain=NCTC13827	GCA_900637235.1	70255	70255	type	True	81.4474	510	920	95	below_threshold
Staphylococcus carnosus	strain=NCTC13825	GCA_900458435.1	1281	1281	type	True	81.4062	523	920	95	below_threshold
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	81.3718	533	920	95	below_threshold
Staphylococcus condimenti	strain=DSM 11674	GCA_001014685.1	70255	70255	type	True	81.2918	489	920	95	below_threshold
Staphylococcus piscifermentans	strain=NCTC13836	GCA_900186985.1	70258	70258	type	True	80.934	507	920	95	below_threshold
Staphylococcus piscifermentans	strain=DSM 7373	GCA_003970555.1	70258	70258	type	True	80.7077	483	920	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	79.274	91	920	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	78.5042	211	920	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.5363	50	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:44,053] [INFO] DFAST Taxonomy check result was written to GCF_900474685.1_40961_B01_genomic.fna/tc_result.tsv
[2024-01-24 11:05:44,054] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:44,054] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:44,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/checkm_data
[2024-01-24 11:05:44,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:44,088] [INFO] Task started: CheckM
[2024-01-24 11:05:44,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900474685.1_40961_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900474685.1_40961_B01_genomic.fna/checkm_input GCF_900474685.1_40961_B01_genomic.fna/checkm_result
[2024-01-24 11:06:09,348] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:09,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,368] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:09,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:09,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900474685.1_40961_B01_genomic.fna/markers.fasta)
[2024-01-24 11:06:09,369] [INFO] Task started: Blastn
[2024-01-24 11:06:09,369] [INFO] Running command: blastn -query GCF_900474685.1_40961_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc768a8a2-1161-448c-a683-52ea031a030e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900474685.1_40961_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:10,168] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:10,171] [INFO] Selected 8 target genomes.
[2024-01-24 11:06:10,171] [INFO] Target genome list was writen to GCF_900474685.1_40961_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:10,177] [INFO] Task started: fastANI
[2024-01-24 11:06:10,178] [INFO] Running command: fastANI --query /var/lib/cwl/stge2146735-13bf-4ffc-b8a7-362231f4d49f/GCF_900474685.1_40961_B01_genomic.fna.gz --refList GCF_900474685.1_40961_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900474685.1_40961_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:15,498] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:15,506] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:15,506] [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_002902285.1	s__Staphylococcus simulans	99.9292	868	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	conclusive
GCF_003043455.1	s__Staphylococcus simulans_A	93.4243	739	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
GCF_002994445.1	s__Staphylococcus simulans_B	83.5221	670	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	96.89	96.89	0.92	0.92	2	-
GCF_001618885.1	s__Staphylococcus condimenti	81.6892	499	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	-
GCF_900458435.1	s__Staphylococcus carnosus	81.4271	524	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCA_900186985.1	s__Staphylococcus piscifermentans	80.9584	505	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003718735.1	s__Staphylococcus debuckii	80.954	501	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001224225.1	s__Staphylococcus borealis	78.9926	225	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:15,508] [INFO] GTDB search result was written to GCF_900474685.1_40961_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:15,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:15,512] [INFO] DFAST_QC result json was written to GCF_900474685.1_40961_B01_genomic.fna/dqc_result.json
[2024-01-24 11:06:15,512] [INFO] DFAST_QC completed!
[2024-01-24 11:06:15,512] [INFO] Total running time: 0h0m47s