[2024-01-24 13:12:52,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,188] [INFO] DQC Reference Directory: /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference
[2024-01-24 13:12:53,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,695] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c824125-091b-46fc-9d5d-bc63b50ef6e3/GCF_900478255.1_34211_E02_genomic.fna.gz | prodigal -d GCF_900478255.1_34211_E02_genomic.fna/cds.fna -a GCF_900478255.1_34211_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:58,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:58,929] [INFO] Task started: HMMsearch
[2024-01-24 13:12:58,930] [INFO] Running command: hmmsearch --tblout GCF_900478255.1_34211_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/reference_markers.hmm GCF_900478255.1_34211_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:59,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:59,218] [INFO] Found 6/6 markers.
[2024-01-24 13:12:59,241] [INFO] Query marker FASTA was written to GCF_900478255.1_34211_E02_genomic.fna/markers.fasta
[2024-01-24 13:12:59,241] [INFO] Task started: Blastn
[2024-01-24 13:12:59,241] [INFO] Running command: blastn -query GCF_900478255.1_34211_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/reference_markers.fasta -out GCF_900478255.1_34211_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:59,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:59,890] [INFO] Selected 20 target genomes.
[2024-01-24 13:12:59,890] [INFO] Target genome list was writen to GCF_900478255.1_34211_E02_genomic.fna/target_genomes.txt
[2024-01-24 13:12:59,918] [INFO] Task started: fastANI
[2024-01-24 13:12:59,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c824125-091b-46fc-9d5d-bc63b50ef6e3/GCF_900478255.1_34211_E02_genomic.fna.gz --refList GCF_900478255.1_34211_E02_genomic.fna/target_genomes.txt --output GCF_900478255.1_34211_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:10,268] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:10,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:10,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:10,282] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:10,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:10,282] [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 lugdunensis	strain=NCTC12217	GCA_900478255.1	28035	28035	type	True	100.0	845	846	95	conclusive
Staphylococcus lugdunensis	strain=NCTC 12217	GCA_002901705.1	28035	28035	type	True	99.9717	836	846	95	conclusive
Staphylococcus warneri	strain=NCTC11044	GCA_900636385.1	1292	1292	type	True	79.5257	320	846	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	79.4659	371	846	95	below_threshold
Staphylococcus haemolyticus	strain=ATCC 29970	GCA_006094395.1	1283	1283	type	True	79.4547	353	846	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.4514	376	846	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	79.4116	352	846	95	below_threshold
Staphylococcus petrasii	strain=CCM 8418	GCA_004684865.1	1276936	1276936	type	True	79.3404	358	846	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	79.2602	353	846	95	below_threshold
Staphylococcus schweitzeri	strain=NCTC13712	GCA_900636685.1	1654388	1654388	type	True	79.2158	299	846	95	below_threshold
Staphylococcus warneri	strain=NCTC 11044	GCA_002901765.1	1292	1292	type	True	79.1153	316	846	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.1133	307	846	95	below_threshold
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	79.0727	338	846	95	below_threshold
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	78.8885	284	846	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	78.8191	326	846	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.5784	301	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:10,284] [INFO] DFAST Taxonomy check result was written to GCF_900478255.1_34211_E02_genomic.fna/tc_result.tsv
[2024-01-24 13:13:10,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:10,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:10,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/checkm_data
[2024-01-24 13:13:10,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:10,316] [INFO] Task started: CheckM
[2024-01-24 13:13:10,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900478255.1_34211_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900478255.1_34211_E02_genomic.fna/checkm_input GCF_900478255.1_34211_E02_genomic.fna/checkm_result
[2024-01-24 13:13:33,429] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:33,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:33,448] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:33,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:33,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900478255.1_34211_E02_genomic.fna/markers.fasta)
[2024-01-24 13:13:33,449] [INFO] Task started: Blastn
[2024-01-24 13:13:33,449] [INFO] Running command: blastn -query GCF_900478255.1_34211_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc296f5b5-8e72-46b2-8372-7bb67ab588d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900478255.1_34211_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:34,188] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:34,191] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:34,191] [INFO] Target genome list was writen to GCF_900478255.1_34211_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:34,205] [INFO] Task started: fastANI
[2024-01-24 13:13:34,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c824125-091b-46fc-9d5d-bc63b50ef6e3/GCF_900478255.1_34211_E02_genomic.fna.gz --refList GCF_900478255.1_34211_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900478255.1_34211_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:42,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:42,567] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:42,568] [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_002901705.1	s__Staphylococcus lugdunensis	99.9717	836	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.51	99.34	0.98	0.96	70	conclusive
GCF_900636385.1	s__Staphylococcus warneri	79.5106	319	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	95.90	0.95	0.90	73	-
GCF_006094395.1	s__Staphylococcus haemolyticus	79.4454	353	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.3941	336	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_004785665.1	s__Staphylococcus pragensis	79.3224	345	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_003035445.1	s__Staphylococcus devriesei_A	79.3075	338	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_001224225.1	s__Staphylococcus borealis	79.3055	344	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002902565.1	s__Staphylococcus petrasii	79.2729	352	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCA_002902575.1	s__Staphylococcus croceilyticus	79.221	342	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902625.1	s__Staphylococcus devriesei	79.0136	309	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_002902405.1	s__Staphylococcus schweitzeri	78.8609	284	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.8061	327	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002902725.1	s__Staphylococcus caprae	78.7615	316	846	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:42,570] [INFO] GTDB search result was written to GCF_900478255.1_34211_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:42,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:42,575] [INFO] DFAST_QC result json was written to GCF_900478255.1_34211_E02_genomic.fna/dqc_result.json
[2024-01-24 13:13:42,575] [INFO] DFAST_QC completed!
[2024-01-24 13:13:42,575] [INFO] Total running time: 0h0m50s