[2024-01-25 17:39:50,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference
[2024-01-25 17:39:51,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,709] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fb1c703-4648-4aac-b0f1-a9678f5abab2/GCF_016642415.1_ASM1664241v1_genomic.fna.gz | prodigal -d GCF_016642415.1_ASM1664241v1_genomic.fna/cds.fna -a GCF_016642415.1_ASM1664241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:56,208] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:56,208] [INFO] Task started: HMMsearch
[2024-01-25 17:39:56,208] [INFO] Running command: hmmsearch --tblout GCF_016642415.1_ASM1664241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/reference_markers.hmm GCF_016642415.1_ASM1664241v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:56,450] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:56,451] [INFO] Found 6/6 markers.
[2024-01-25 17:39:56,470] [INFO] Query marker FASTA was written to GCF_016642415.1_ASM1664241v1_genomic.fna/markers.fasta
[2024-01-25 17:39:56,471] [INFO] Task started: Blastn
[2024-01-25 17:39:56,471] [INFO] Running command: blastn -query GCF_016642415.1_ASM1664241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/reference_markers.fasta -out GCF_016642415.1_ASM1664241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:57,050] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:57,053] [INFO] Selected 13 target genomes.
[2024-01-25 17:39:57,053] [INFO] Target genome list was writen to GCF_016642415.1_ASM1664241v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:57,077] [INFO] Task started: fastANI
[2024-01-25 17:39:57,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb1c703-4648-4aac-b0f1-a9678f5abab2/GCF_016642415.1_ASM1664241v1_genomic.fna.gz --refList GCF_016642415.1_ASM1664241v1_genomic.fna/target_genomes.txt --output GCF_016642415.1_ASM1664241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:03,507] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:03,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:03,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:03,517] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:03,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:03,517] [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 rubneri	strain=DSM 26920	GCA_004785935.1	1234680	1234680	type	True	99.9859	705	705	95	conclusive
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	91.6783	575	705	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	91.6248	573	705	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000222745.2	113107	113107	type	True	91.5212	568	705	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	90.2139	541	705	95	below_threshold
Streptococcus ilei	strain=I-G2	GCA_000479335.1	1156431	1156431	type	True	90.0698	571	705	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	84.9186	415	705	95	below_threshold
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	84.7703	426	705	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	81.1217	217	705	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	81.0968	217	705	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.9113	103	705	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.3084	69	705	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.2739	97	705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:03,518] [INFO] DFAST Taxonomy check result was written to GCF_016642415.1_ASM1664241v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:03,519] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:03,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:03,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/checkm_data
[2024-01-25 17:40:03,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:03,544] [INFO] Task started: CheckM
[2024-01-25 17:40:03,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016642415.1_ASM1664241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016642415.1_ASM1664241v1_genomic.fna/checkm_input GCF_016642415.1_ASM1664241v1_genomic.fna/checkm_result
[2024-01-25 17:40:22,893] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:22,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:22,916] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:22,916] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:22,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016642415.1_ASM1664241v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:22,917] [INFO] Task started: Blastn
[2024-01-25 17:40:22,917] [INFO] Running command: blastn -query GCF_016642415.1_ASM1664241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41b9df2d-d077-4cb1-9134-c09344ca51b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016642415.1_ASM1664241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:23,744] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:23,747] [INFO] Selected 12 target genomes.
[2024-01-25 17:40:23,748] [INFO] Target genome list was writen to GCF_016642415.1_ASM1664241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:23,762] [INFO] Task started: fastANI
[2024-01-25 17:40:23,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb1c703-4648-4aac-b0f1-a9678f5abab2/GCF_016642415.1_ASM1664241v1_genomic.fna.gz --refList GCF_016642415.1_ASM1664241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016642415.1_ASM1664241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:29,680] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:29,689] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:29,689] [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_004785935.1	s__Streptococcus rubneri	99.9859	705	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.13	96.92	0.96	0.90	4	conclusive
GCF_000186465.1	s__Streptococcus australis	91.6889	574	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.56	95.15	0.93	0.86	5	-
GCF_004166885.1	s__Streptococcus sp004166885	90.3792	551	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.19	95.32	0.93	0.91	8	-
GCF_015553625.1	s__Streptococcus australis_B	90.2447	548	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.97	95.85	0.92	0.90	3	-
GCF_006385805.1	s__Streptococcus xiaochunlingii	90.2139	541	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.12	95.36	0.92	0.90	9	-
GCA_902363395.1	s__Streptococcus sp902363395	90.1395	545	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627135.1	s__Streptococcus koreensis	89.9611	563	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.43	95.11	0.91	0.89	8	-
GCA_902836505.1	s__Streptococcus sp902836505	89.4561	274	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314795.2	s__Streptococcus sp000314795	86.8126	443	705	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	85.298	231	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000180035.1	s__Streptococcus parasanguinis_C	84.9125	421	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.27	96.01	0.92	0.90	7	-
GCF_016642265.1	s__Streptococcus lactarius	83.7066	362	705	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.47	95.23	0.92	0.88	8	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:29,690] [INFO] GTDB search result was written to GCF_016642415.1_ASM1664241v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:29,691] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:29,700] [INFO] DFAST_QC result json was written to GCF_016642415.1_ASM1664241v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:29,700] [INFO] DFAST_QC completed!
[2024-01-25 17:40:29,700] [INFO] Total running time: 0h0m39s