[2024-01-24 12:36:22,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:22,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:22,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference
[2024-01-24 12:36:24,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:24,135] [INFO] Task started: Prodigal
[2024-01-24 12:36:24,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg562fbbfe-89e4-424b-82aa-79af32e7be81/GCF_024814435.1_ASM2481443v1_genomic.fna.gz | prodigal -d GCF_024814435.1_ASM2481443v1_genomic.fna/cds.fna -a GCF_024814435.1_ASM2481443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:29,121] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:29,121] [INFO] Task started: HMMsearch
[2024-01-24 12:36:29,122] [INFO] Running command: hmmsearch --tblout GCF_024814435.1_ASM2481443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/reference_markers.hmm GCF_024814435.1_ASM2481443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:29,352] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:29,354] [INFO] Found 6/6 markers.
[2024-01-24 12:36:29,377] [INFO] Query marker FASTA was written to GCF_024814435.1_ASM2481443v1_genomic.fna/markers.fasta
[2024-01-24 12:36:29,378] [INFO] Task started: Blastn
[2024-01-24 12:36:29,378] [INFO] Running command: blastn -query GCF_024814435.1_ASM2481443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/reference_markers.fasta -out GCF_024814435.1_ASM2481443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:29,971] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:29,975] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:29,975] [INFO] Target genome list was writen to GCF_024814435.1_ASM2481443v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:30,045] [INFO] Task started: fastANI
[2024-01-24 12:36:30,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg562fbbfe-89e4-424b-82aa-79af32e7be81/GCF_024814435.1_ASM2481443v1_genomic.fna.gz --refList GCF_024814435.1_ASM2481443v1_genomic.fna/target_genomes.txt --output GCF_024814435.1_ASM2481443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:36,042] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:36,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:36,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:36,057] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:36,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:36,057] [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 rostri	strain=DSM 21968	GCA_002902145.1	522262	522262	type	True	84.21	571	734	95	below_threshold
Staphylococcus microti	strain=DSM 22147	GCA_002902635.1	569857	569857	type	True	83.0145	507	734	95	below_threshold
Staphylococcus microti	strain=DSM 22147	GCA_000934465.1	569857	569857	type	True	82.9035	510	734	95	below_threshold
Staphylococcus microti	strain=NCTC13832	GCA_900458705.1	569857	569857	type	True	82.8195	541	734	95	below_threshold
Staphylococcus muscae	strain=ATCC 49910	GCA_003019275.1	1294	1294	type	True	81.1517	444	734	95	below_threshold
Staphylococcus muscae	strain=NCTC13833	GCA_900187005.1	1294	1294	type	True	81.0712	451	734	95	below_threshold
Staphylococcus muscae	strain=DSM 7068	GCA_002901905.1	1294	1294	type	True	81.0617	425	734	95	below_threshold
Staphylococcus muscae	strain=CCM 4175	GCA_014634965.1	1294	1294	type	True	81.0437	444	734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:36,060] [INFO] DFAST Taxonomy check result was written to GCF_024814435.1_ASM2481443v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:36,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:36,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:36,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/checkm_data
[2024-01-24 12:36:36,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:36,089] [INFO] Task started: CheckM
[2024-01-24 12:36:36,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024814435.1_ASM2481443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024814435.1_ASM2481443v1_genomic.fna/checkm_input GCF_024814435.1_ASM2481443v1_genomic.fna/checkm_result
[2024-01-24 12:36:58,016] [INFO] Task succeeded: CheckM
[2024-01-24 12:36:58,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:36:58,034] [INFO] ===== Completeness check finished =====
[2024-01-24 12:36:58,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:36:58,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024814435.1_ASM2481443v1_genomic.fna/markers.fasta)
[2024-01-24 12:36:58,036] [INFO] Task started: Blastn
[2024-01-24 12:36:58,036] [INFO] Running command: blastn -query GCF_024814435.1_ASM2481443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96089575-ec11-44d6-9d54-0406af30615d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024814435.1_ASM2481443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:58,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:58,821] [INFO] Selected 17 target genomes.
[2024-01-24 12:36:58,821] [INFO] Target genome list was writen to GCF_024814435.1_ASM2481443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:58,844] [INFO] Task started: fastANI
[2024-01-24 12:36:58,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg562fbbfe-89e4-424b-82aa-79af32e7be81/GCF_024814435.1_ASM2481443v1_genomic.fna.gz --refList GCF_024814435.1_ASM2481443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024814435.1_ASM2481443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:06,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:06,203] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:37:06,203] [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_002902145.1	s__Staphylococcus rostri	84.2245	569	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934465.1	s__Staphylococcus microti	82.898	509	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_003019275.1	s__Staphylococcus muscae	81.1374	445	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	-
GCF_013463155.1	s__Staphylococcus sp013463155	79.8202	365	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	79.0209	237	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.9665	257	734	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	78.9252	281	734	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	78.9084	254	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_002101335.1	s__Staphylococcus lutrae	78.791	201	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016238445.1	s__Staphylococcus sp016238445	78.7312	202	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901995.1	s__Staphylococcus coagulans	78.7244	222	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_003012915.1	s__Staphylococcus felis	78.6341	226	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCF_002901865.1	s__Staphylococcus agnetis	78.5732	221	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_004785665.1	s__Staphylococcus pragensis	78.5194	127	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.1789	134	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCA_002902575.1	s__Staphylococcus croceilyticus	78.0976	143	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902565.1	s__Staphylococcus petrasii	77.9509	135	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:06,205] [INFO] GTDB search result was written to GCF_024814435.1_ASM2481443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:06,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:06,209] [INFO] DFAST_QC result json was written to GCF_024814435.1_ASM2481443v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:06,209] [INFO] DFAST_QC completed!
[2024-01-24 12:37:06,209] [INFO] Total running time: 0h0m43s