[2024-01-24 12:52:51,113] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference
[2024-01-24 12:52:53,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,758] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg964f7860-cf9b-42f5-ad32-a26052d83027/GCF_900187005.1_50569_B01_genomic.fna.gz | prodigal -d GCF_900187005.1_50569_B01_genomic.fna/cds.fna -a GCF_900187005.1_50569_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:58,609] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:58,609] [INFO] Task started: HMMsearch
[2024-01-24 12:52:58,609] [INFO] Running command: hmmsearch --tblout GCF_900187005.1_50569_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/reference_markers.hmm GCF_900187005.1_50569_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:58,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:58,869] [INFO] Found 6/6 markers.
[2024-01-24 12:52:58,889] [INFO] Query marker FASTA was written to GCF_900187005.1_50569_B01_genomic.fna/markers.fasta
[2024-01-24 12:52:58,890] [INFO] Task started: Blastn
[2024-01-24 12:52:58,890] [INFO] Running command: blastn -query GCF_900187005.1_50569_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/reference_markers.fasta -out GCF_900187005.1_50569_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:00,556] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:00,561] [INFO] Selected 11 target genomes.
[2024-01-24 12:53:00,561] [INFO] Target genome list was writen to GCF_900187005.1_50569_B01_genomic.fna/target_genomes.txt
[2024-01-24 12:53:00,654] [INFO] Task started: fastANI
[2024-01-24 12:53:00,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg964f7860-cf9b-42f5-ad32-a26052d83027/GCF_900187005.1_50569_B01_genomic.fna.gz --refList GCF_900187005.1_50569_B01_genomic.fna/target_genomes.txt --output GCF_900187005.1_50569_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:06,477] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:06,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:06,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:06,491] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:53:06,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:06,491] [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 muscae	strain=NCTC13833	GCA_900187005.1	1294	1294	type	True	100.0	697	698	95	conclusive
Staphylococcus muscae	strain=ATCC 49910	GCA_003019275.1	1294	1294	type	True	99.9956	696	698	95	conclusive
Staphylococcus muscae	strain=CCM 4175	GCA_014634965.1	1294	1294	type	True	99.9761	671	698	95	conclusive
Staphylococcus muscae	strain=DSM 7068	GCA_002901905.1	1294	1294	type	True	99.8651	608	698	95	conclusive
Staphylococcus microti	strain=NCTC13832	GCA_900458705.1	569857	569857	type	True	82.1242	507	698	95	below_threshold
Staphylococcus rostri	strain=DSM 21968	GCA_002902145.1	522262	522262	type	True	81.7652	502	698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:06,493] [INFO] DFAST Taxonomy check result was written to GCF_900187005.1_50569_B01_genomic.fna/tc_result.tsv
[2024-01-24 12:53:06,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:06,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:06,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/checkm_data
[2024-01-24 12:53:06,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:06,524] [INFO] Task started: CheckM
[2024-01-24 12:53:06,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187005.1_50569_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187005.1_50569_B01_genomic.fna/checkm_input GCF_900187005.1_50569_B01_genomic.fna/checkm_result
[2024-01-24 12:53:29,625] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:29,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:29,649] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:29,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:29,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187005.1_50569_B01_genomic.fna/markers.fasta)
[2024-01-24 12:53:29,650] [INFO] Task started: Blastn
[2024-01-24 12:53:29,650] [INFO] Running command: blastn -query GCF_900187005.1_50569_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a9e29a-b2ff-451d-ab4a-b4222854ca50/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187005.1_50569_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:30,416] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:30,420] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:30,420] [INFO] Target genome list was writen to GCF_900187005.1_50569_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:30,446] [INFO] Task started: fastANI
[2024-01-24 12:53:30,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg964f7860-cf9b-42f5-ad32-a26052d83027/GCF_900187005.1_50569_B01_genomic.fna.gz --refList GCF_900187005.1_50569_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187005.1_50569_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:37,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:37,091] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:37,091] [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_003019275.1	s__Staphylococcus muscae	99.9956	695	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_000934465.1	s__Staphylococcus microti	81.8305	501	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002902145.1	s__Staphylococcus rostri	81.7524	502	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013463155.1	s__Staphylococcus sp013463155	80.2922	365	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636325.1	s__Staphylococcus delphini	79.739	260	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_000816085.1	s__Staphylococcus hyicus	79.5199	229	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_010365305.1	s__Staphylococcus sp010365305	79.3723	261	698	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	79.1657	252	698	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	79.0956	252	698	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	78.8724	232	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_003718735.1	s__Staphylococcus debuckii	78.662	153	698	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	78.181	141	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002902085.1	s__Staphylococcus simiae	77.8615	150	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_002902235.1	s__Staphylococcus ureilyticus	77.8058	134	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:37,093] [INFO] GTDB search result was written to GCF_900187005.1_50569_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:37,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:37,096] [INFO] DFAST_QC result json was written to GCF_900187005.1_50569_B01_genomic.fna/dqc_result.json
[2024-01-24 12:53:37,097] [INFO] DFAST_QC completed!
[2024-01-24 12:53:37,097] [INFO] Total running time: 0h0m46s