[2023-06-18 12:03:44,889] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:03:44,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:03:44,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference
[2023-06-18 12:03:46,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:03:46,231] [INFO] Task started: Prodigal
[2023-06-18 12:03:46,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac2ea5a-85e2-4243-bea6-83e8d25ffe53/GCA_018371015.1_ASM1837101v1_genomic.fna.gz | prodigal -d GCA_018371015.1_ASM1837101v1_genomic.fna/cds.fna -a GCA_018371015.1_ASM1837101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:03:50,753] [INFO] Task succeeded: Prodigal
[2023-06-18 12:03:50,754] [INFO] Task started: HMMsearch
[2023-06-18 12:03:50,754] [INFO] Running command: hmmsearch --tblout GCA_018371015.1_ASM1837101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/reference_markers.hmm GCA_018371015.1_ASM1837101v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:03:51,004] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:03:51,006] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ac2ea5a-85e2-4243-bea6-83e8d25ffe53/GCA_018371015.1_ASM1837101v1_genomic.fna.gz]
[2023-06-18 12:03:51,034] [INFO] Query marker FASTA was written to GCA_018371015.1_ASM1837101v1_genomic.fna/markers.fasta
[2023-06-18 12:03:51,034] [INFO] Task started: Blastn
[2023-06-18 12:03:51,034] [INFO] Running command: blastn -query GCA_018371015.1_ASM1837101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/reference_markers.fasta -out GCA_018371015.1_ASM1837101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:03:51,647] [INFO] Task succeeded: Blastn
[2023-06-18 12:03:51,652] [INFO] Selected 14 target genomes.
[2023-06-18 12:03:51,653] [INFO] Target genome list was writen to GCA_018371015.1_ASM1837101v1_genomic.fna/target_genomes.txt
[2023-06-18 12:03:51,658] [INFO] Task started: fastANI
[2023-06-18 12:03:51,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac2ea5a-85e2-4243-bea6-83e8d25ffe53/GCA_018371015.1_ASM1837101v1_genomic.fna.gz --refList GCA_018371015.1_ASM1837101v1_genomic.fna/target_genomes.txt --output GCA_018371015.1_ASM1837101v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:03:58,001] [INFO] Task succeeded: fastANI
[2023-06-18 12:03:58,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:03:58,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:03:58,016] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:03:58,017] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 12:03:58,017] [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	88.5734	494	622	95	below_threshold
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	88.5723	491	622	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	84.5796	367	622	95	below_threshold
Streptococcus rubneri	strain=DSM 26920	GCA_004785935.1	1234680	1234680	type	True	84.3785	359	622	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	84.3514	356	622	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	84.1914	338	622	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	84.089	351	622	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	80.4968	178	622	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.3647	180	622	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.0807	186	622	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	80.0107	206	622	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	79.9364	178	622	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	77.8733	104	622	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	77.6836	78	622	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:03:58,019] [INFO] DFAST Taxonomy check result was written to GCA_018371015.1_ASM1837101v1_genomic.fna/tc_result.tsv
[2023-06-18 12:03:58,020] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:03:58,020] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:03:58,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/checkm_data
[2023-06-18 12:03:58,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:03:58,050] [INFO] Task started: CheckM
[2023-06-18 12:03:58,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018371015.1_ASM1837101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018371015.1_ASM1837101v1_genomic.fna/checkm_input GCA_018371015.1_ASM1837101v1_genomic.fna/checkm_result
[2023-06-18 12:04:19,427] [INFO] Task succeeded: CheckM
[2023-06-18 12:04:19,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:04:19,456] [INFO] ===== Completeness check finished =====
[2023-06-18 12:04:19,457] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:04:19,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018371015.1_ASM1837101v1_genomic.fna/markers.fasta)
[2023-06-18 12:04:19,457] [INFO] Task started: Blastn
[2023-06-18 12:04:19,458] [INFO] Running command: blastn -query GCA_018371015.1_ASM1837101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967b320d-b545-4b27-88bf-7883a86d8522/dqc_reference/reference_markers_gtdb.fasta -out GCA_018371015.1_ASM1837101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:04:20,404] [INFO] Task succeeded: Blastn
[2023-06-18 12:04:20,409] [INFO] Selected 14 target genomes.
[2023-06-18 12:04:20,409] [INFO] Target genome list was writen to GCA_018371015.1_ASM1837101v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:04:20,422] [INFO] Task started: fastANI
[2023-06-18 12:04:20,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac2ea5a-85e2-4243-bea6-83e8d25ffe53/GCA_018371015.1_ASM1837101v1_genomic.fna.gz --refList GCA_018371015.1_ASM1837101v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018371015.1_ASM1837101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:04:28,783] [INFO] Task succeeded: fastANI
[2023-06-18 12:04:28,806] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:04:28,807] [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	95.7539	546	622	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	92.5555	520	622	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	92.3829	396	622	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	89.444	281	622	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	89.409	490	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0331	95.56	95.56	0.87	0.87	2	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	89.2626	505	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCF_016648925.1	s__Streptococcus sp900766505	89.2184	499	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	-
GCA_000180035.1	s__Streptococcus parasanguinis_C	88.9907	491	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.27	96.01	0.92	0.90	7	-
GCF_009717815.1	s__Streptococcus parasanguinis_F	88.899	504	622	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	88.681	518	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2593	95.62	95.52	0.88	0.87	6	-
GCF_000164675.2	s__Streptococcus parasanguinis	88.5818	494	622	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	88.2904	501	622	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	84.6704	355	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.56	95.15	0.93	0.86	5	-
GCF_003627135.1	s__Streptococcus koreensis	84.2824	361	622	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.43	95.11	0.91	0.89	8	-
--------------------------------------------------------------------------------
[2023-06-18 12:04:28,809] [INFO] GTDB search result was written to GCA_018371015.1_ASM1837101v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:04:28,809] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:04:28,812] [INFO] DFAST_QC result json was written to GCA_018371015.1_ASM1837101v1_genomic.fna/dqc_result.json
[2023-06-18 12:04:28,813] [INFO] DFAST_QC completed!
[2023-06-18 12:04:28,813] [INFO] Total running time: 0h0m44s