[2024-01-24 11:34:41,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference
[2024-01-24 11:34:42,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,698] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg80576703-655b-41a0-884e-a1b34992996c/GCF_016642265.1_ASM1664226v1_genomic.fna.gz | prodigal -d GCF_016642265.1_ASM1664226v1_genomic.fna/cds.fna -a GCF_016642265.1_ASM1664226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:48,062] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:48,062] [INFO] Task started: HMMsearch
[2024-01-24 11:34:48,062] [INFO] Running command: hmmsearch --tblout GCF_016642265.1_ASM1664226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/reference_markers.hmm GCF_016642265.1_ASM1664226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:48,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:48,308] [INFO] Found 6/6 markers.
[2024-01-24 11:34:48,327] [INFO] Query marker FASTA was written to GCF_016642265.1_ASM1664226v1_genomic.fna/markers.fasta
[2024-01-24 11:34:48,327] [INFO] Task started: Blastn
[2024-01-24 11:34:48,328] [INFO] Running command: blastn -query GCF_016642265.1_ASM1664226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/reference_markers.fasta -out GCF_016642265.1_ASM1664226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:48,913] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:48,916] [INFO] Selected 20 target genomes.
[2024-01-24 11:34:48,917] [INFO] Target genome list was writen to GCF_016642265.1_ASM1664226v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:48,937] [INFO] Task started: fastANI
[2024-01-24 11:34:48,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg80576703-655b-41a0-884e-a1b34992996c/GCF_016642265.1_ASM1664226v1_genomic.fna.gz --refList GCF_016642265.1_ASM1664226v1_genomic.fna/target_genomes.txt --output GCF_016642265.1_ASM1664226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:56,653] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:56,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:56,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:56,668] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:34:56,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:34:56,668] [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
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	88.121	527	694	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	88.0723	524	694	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	84.1803	376	694	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	84.1084	374	694	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	84.0326	353	694	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	83.9571	376	694	95	below_threshold
Streptococcus rubneri	strain=DSM 26920	GCA_004785935.1	1234680	1234680	type	True	83.9446	366	694	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	83.7982	359	694	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	80.8838	214	694	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.3273	192	694	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	80.2856	193	694	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	80.1125	185	694	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	80.1064	106	694	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.7028	66	694	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.4108	94	694	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.356	81	694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:56,670] [INFO] DFAST Taxonomy check result was written to GCF_016642265.1_ASM1664226v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:56,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:56,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:56,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/checkm_data
[2024-01-24 11:34:56,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:56,696] [INFO] Task started: CheckM
[2024-01-24 11:34:56,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016642265.1_ASM1664226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016642265.1_ASM1664226v1_genomic.fna/checkm_input GCF_016642265.1_ASM1664226v1_genomic.fna/checkm_result
[2024-01-24 11:35:19,363] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:19,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:19,382] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:19,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:19,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016642265.1_ASM1664226v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:19,383] [INFO] Task started: Blastn
[2024-01-24 11:35:19,383] [INFO] Running command: blastn -query GCF_016642265.1_ASM1664226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f4ce630-bc8a-4ec6-afd8-7b7490903cf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016642265.1_ASM1664226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:20,282] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:20,286] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:20,286] [INFO] Target genome list was writen to GCF_016642265.1_ASM1664226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:20,342] [INFO] Task started: fastANI
[2024-01-24 11:35:20,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg80576703-655b-41a0-884e-a1b34992996c/GCF_016642265.1_ASM1664226v1_genomic.fna.gz --refList GCF_016642265.1_ASM1664226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016642265.1_ASM1664226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:28,560] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:28,572] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:28,572] [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_016642265.1	s__Streptococcus lactarius	100.0	693	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.47	95.23	0.92	0.88	8	conclusive
GCF_901875555.1	s__Streptococcus parasanguinis_H	93.0365	551	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755085.1	s__Streptococcus sp900755085	91.4834	416	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373455.1	s__Streptococcus sp902373455	88.9349	278	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018365265.1	s__Streptococcus parasanguinis_G	88.8854	522	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0331	95.56	95.56	0.87	0.87	2	-
GCF_001074805.1	s__Streptococcus parasanguinis_A	88.8085	507	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016648925.1	s__Streptococcus sp900766505	88.7483	531	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	-
GCF_001073155.1	s__Streptococcus parasanguinis_D	88.65	526	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.84	96.67	0.91	0.89	4	-
GCF_009717815.1	s__Streptococcus parasanguinis_F	88.4897	529	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.25	95.86	95.53	0.89	0.86	10	-
GCF_001813295.1	s__Streptococcus sp001813295	88.2908	546	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2593	95.62	95.52	0.88	0.87	6	-
GCA_000180035.1	s__Streptococcus parasanguinis_C	88.0947	523	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.27	96.01	0.92	0.90	7	-
GCF_000164675.2	s__Streptococcus parasanguinis	88.0723	524	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.96	95.18	0.90	0.85	22	-
GCF_000314795.2	s__Streptococcus sp000314795	87.9016	530	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186465.1	s__Streptococcus australis	84.1447	373	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.56	95.15	0.93	0.86	5	-
GCF_011421455.1	s__Streptococcus catagoni	78.6604	66	694	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:28,573] [INFO] GTDB search result was written to GCF_016642265.1_ASM1664226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:28,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:28,577] [INFO] DFAST_QC result json was written to GCF_016642265.1_ASM1664226v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:28,577] [INFO] DFAST_QC completed!
[2024-01-24 11:35:28,578] [INFO] Total running time: 0h0m47s