[2023-06-19 07:50:07,782] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:50:07,783] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:50:07,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference
[2023-06-19 07:50:09,040] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:50:09,041] [INFO] Task started: Prodigal
[2023-06-19 07:50:09,042] [INFO] Running command: gunzip -c /var/lib/cwl/stge85014fd-dcb5-4608-9ea1-7cbabca8c9c6/GCA_018381295.1_ASM1838129v1_genomic.fna.gz | prodigal -d GCA_018381295.1_ASM1838129v1_genomic.fna/cds.fna -a GCA_018381295.1_ASM1838129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:50:13,672] [INFO] Task succeeded: Prodigal
[2023-06-19 07:50:13,672] [INFO] Task started: HMMsearch
[2023-06-19 07:50:13,673] [INFO] Running command: hmmsearch --tblout GCA_018381295.1_ASM1838129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/reference_markers.hmm GCA_018381295.1_ASM1838129v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:50:13,948] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:50:13,950] [INFO] Found 6/6 markers.
[2023-06-19 07:50:13,975] [INFO] Query marker FASTA was written to GCA_018381295.1_ASM1838129v1_genomic.fna/markers.fasta
[2023-06-19 07:50:13,975] [INFO] Task started: Blastn
[2023-06-19 07:50:13,975] [INFO] Running command: blastn -query GCA_018381295.1_ASM1838129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/reference_markers.fasta -out GCA_018381295.1_ASM1838129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:14,573] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:14,576] [INFO] Selected 14 target genomes.
[2023-06-19 07:50:14,576] [INFO] Target genome list was writen to GCA_018381295.1_ASM1838129v1_genomic.fna/target_genomes.txt
[2023-06-19 07:50:14,579] [INFO] Task started: fastANI
[2023-06-19 07:50:14,579] [INFO] Running command: fastANI --query /var/lib/cwl/stge85014fd-dcb5-4608-9ea1-7cbabca8c9c6/GCA_018381295.1_ASM1838129v1_genomic.fna.gz --refList GCA_018381295.1_ASM1838129v1_genomic.fna/target_genomes.txt --output GCA_018381295.1_ASM1838129v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:50:20,901] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:20,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:50:20,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:50:20,913] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:50:20,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:50:20,914] [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=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	93.9126	546	632	95	below_threshold
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	93.912	544	632	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000222745.2	113107	113107	type	True	85.258	388	632	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	85.2535	392	632	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	85.2067	384	632	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	84.8968	374	632	95	below_threshold
Streptococcus rubneri	strain=DSM 26920	GCA_004785935.1	1234680	1234680	type	True	84.8872	394	632	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	84.8689	376	632	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	84.789	396	632	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	79.8155	187	632	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.7879	192	632	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	77.878	91	632	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.7915	80	632	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	76.8492	76	632	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:50:20,915] [INFO] DFAST Taxonomy check result was written to GCA_018381295.1_ASM1838129v1_genomic.fna/tc_result.tsv
[2023-06-19 07:50:20,916] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:50:20,916] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:50:20,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/checkm_data
[2023-06-19 07:50:20,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:50:20,939] [INFO] Task started: CheckM
[2023-06-19 07:50:20,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381295.1_ASM1838129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381295.1_ASM1838129v1_genomic.fna/checkm_input GCA_018381295.1_ASM1838129v1_genomic.fna/checkm_result
[2023-06-19 07:50:42,523] [INFO] Task succeeded: CheckM
[2023-06-19 07:50:42,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:50:42,556] [INFO] ===== Completeness check finished =====
[2023-06-19 07:50:42,557] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:50:42,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381295.1_ASM1838129v1_genomic.fna/markers.fasta)
[2023-06-19 07:50:42,557] [INFO] Task started: Blastn
[2023-06-19 07:50:42,557] [INFO] Running command: blastn -query GCA_018381295.1_ASM1838129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg931b71cd-b60b-41ed-bfb0-873883b5c4b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381295.1_ASM1838129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:43,409] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:43,415] [INFO] Selected 16 target genomes.
[2023-06-19 07:50:43,416] [INFO] Target genome list was writen to GCA_018381295.1_ASM1838129v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:50:43,425] [INFO] Task started: fastANI
[2023-06-19 07:50:43,425] [INFO] Running command: fastANI --query /var/lib/cwl/stge85014fd-dcb5-4608-9ea1-7cbabca8c9c6/GCA_018381295.1_ASM1838129v1_genomic.fna.gz --refList GCA_018381295.1_ASM1838129v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381295.1_ASM1838129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:50:52,624] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:52,638] [INFO] Found 16 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-19 07:50:52,638] [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
GCA_018365265.1	s__Streptococcus parasanguinis_G	95.5577	549	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0331	95.56	95.56	0.87	0.87	2	inconclusive
GCF_016648925.1	s__Streptococcus sp900766505	95.33	559	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	inconclusive
GCF_000448565.1	s__Streptococcus sp000448565	95.128	581	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2003	N/A	N/A	N/A	N/A	1	-
GCF_001073155.1	s__Streptococcus parasanguinis_D	95.0482	537	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.84	96.67	0.91	0.89	4	inconclusive
GCA_018366675.1	s__Streptococcus parasanguinis_E	94.9359	491	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.293	95.61	95.45	0.89	0.84	13	-
GCF_001813295.1	s__Streptococcus sp001813295	94.8835	567	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2593	95.62	95.52	0.88	0.87	6	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	94.8088	578	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCF_009717815.1	s__Streptococcus parasanguinis_F	94.7699	561	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.25	95.86	95.53	0.89	0.86	10	-
GCA_000180035.1	s__Streptococcus parasanguinis_C	94.5248	561	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.27	96.01	0.92	0.90	7	-
GCF_001074805.1	s__Streptococcus parasanguinis_A	94.0231	532	632	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	93.9717	313	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164675.2	s__Streptococcus parasanguinis	93.8769	547	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.96	95.18	0.90	0.85	22	-
GCF_000186465.1	s__Streptococcus australis	85.2517	382	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.56	95.15	0.93	0.86	5	-
GCF_006385805.1	s__Streptococcus xiaochunlingii	84.9487	373	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.12	95.36	0.92	0.90	9	-
GCF_004785935.1	s__Streptococcus rubneri	84.8802	394	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.13	96.92	0.96	0.90	4	-
GCF_015553625.1	s__Streptococcus australis_B	84.6069	386	632	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.97	95.85	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-19 07:50:52,641] [INFO] GTDB search result was written to GCA_018381295.1_ASM1838129v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:50:52,642] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:50:52,646] [INFO] DFAST_QC result json was written to GCA_018381295.1_ASM1838129v1_genomic.fna/dqc_result.json
[2023-06-19 07:50:52,646] [INFO] DFAST_QC completed!
[2023-06-19 07:50:52,646] [INFO] Total running time: 0h0m45s