[2024-01-25 20:15:50,364] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:50,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:50,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference
[2024-01-25 20:15:51,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:51,529] [INFO] Task started: Prodigal
[2024-01-25 20:15:51,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg754d7340-6195-40bc-86ad-3c14036916e2/GCF_003718735.1_ASM371873v1_genomic.fna.gz | prodigal -d GCF_003718735.1_ASM371873v1_genomic.fna/cds.fna -a GCF_003718735.1_ASM371873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:56,438] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:56,439] [INFO] Task started: HMMsearch
[2024-01-25 20:15:56,439] [INFO] Running command: hmmsearch --tblout GCF_003718735.1_ASM371873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/reference_markers.hmm GCF_003718735.1_ASM371873v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:56,656] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:56,657] [INFO] Found 6/6 markers.
[2024-01-25 20:15:56,680] [INFO] Query marker FASTA was written to GCF_003718735.1_ASM371873v1_genomic.fna/markers.fasta
[2024-01-25 20:15:56,680] [INFO] Task started: Blastn
[2024-01-25 20:15:56,680] [INFO] Running command: blastn -query GCF_003718735.1_ASM371873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/reference_markers.fasta -out GCF_003718735.1_ASM371873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:57,253] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:57,255] [INFO] Selected 12 target genomes.
[2024-01-25 20:15:57,255] [INFO] Target genome list was writen to GCF_003718735.1_ASM371873v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:57,257] [INFO] Task started: fastANI
[2024-01-25 20:15:57,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg754d7340-6195-40bc-86ad-3c14036916e2/GCF_003718735.1_ASM371873v1_genomic.fna.gz --refList GCF_003718735.1_ASM371873v1_genomic.fna/target_genomes.txt --output GCF_003718735.1_ASM371873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:04,259] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:04,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:04,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:04,268] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:04,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:04,268] [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 debuckii	strain=SDB 2975	GCA_003718735.1	2044912	2044912	type	True	100.0	896	897	95	conclusive
Staphylococcus piscifermentans	strain=NCTC13836	GCA_900186985.1	70258	70258	type	True	94.7141	788	897	95	below_threshold
Staphylococcus piscifermentans	strain=DSM 7373	GCA_003970555.1	70258	70258	type	True	94.5984	735	897	95	below_threshold
Staphylococcus carnosus	strain=NCTC13825	GCA_900458435.1	1281	1281	type	True	85.238	699	897	95	below_threshold
Staphylococcus condimenti	strain=DSM 11674	GCA_001618885.1	70255	70255	type	True	85.1874	717	897	95	below_threshold
Staphylococcus condimenti	strain=NCTC13827	GCA_900637235.1	70255	70255	type	True	85.1711	718	897	95	below_threshold
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	85.1384	716	897	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	79.5637	147	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:04,269] [INFO] DFAST Taxonomy check result was written to GCF_003718735.1_ASM371873v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:04,270] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:04,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:04,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/checkm_data
[2024-01-25 20:16:04,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:04,299] [INFO] Task started: CheckM
[2024-01-25 20:16:04,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003718735.1_ASM371873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003718735.1_ASM371873v1_genomic.fna/checkm_input GCF_003718735.1_ASM371873v1_genomic.fna/checkm_result
[2024-01-25 20:16:24,980] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:24,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.72%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:25,003] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:25,003] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:25,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003718735.1_ASM371873v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:25,004] [INFO] Task started: Blastn
[2024-01-25 20:16:25,004] [INFO] Running command: blastn -query GCF_003718735.1_ASM371873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87dcac74-509e-47b3-b9b0-32ebb93ddc4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003718735.1_ASM371873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:25,766] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:25,769] [INFO] Selected 8 target genomes.
[2024-01-25 20:16:25,770] [INFO] Target genome list was writen to GCF_003718735.1_ASM371873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:25,771] [INFO] Task started: fastANI
[2024-01-25 20:16:25,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg754d7340-6195-40bc-86ad-3c14036916e2/GCF_003718735.1_ASM371873v1_genomic.fna.gz --refList GCF_003718735.1_ASM371873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003718735.1_ASM371873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:30,733] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:30,740] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:30,740] [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_003718735.1	s__Staphylococcus debuckii	100.0	895	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900186985.1	s__Staphylococcus piscifermentans	94.6919	789	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_900458435.1	s__Staphylococcus carnosus	85.238	699	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCF_001618885.1	s__Staphylococcus condimenti	85.1874	717	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	-
GCF_002902285.1	s__Staphylococcus simulans	81.0461	483	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_003043455.1	s__Staphylococcus simulans_A	80.9112	451	897	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	80.8668	477	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	96.89	96.89	0.92	0.92	2	-
GCF_003019275.1	s__Staphylococcus muscae	78.7093	152	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:30,742] [INFO] GTDB search result was written to GCF_003718735.1_ASM371873v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:30,742] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:30,744] [INFO] DFAST_QC result json was written to GCF_003718735.1_ASM371873v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:30,744] [INFO] DFAST_QC completed!
[2024-01-25 20:16:30,744] [INFO] Total running time: 0h0m40s