[2023-06-19 10:05:47,049] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:05:47,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:05:47,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference
[2023-06-19 10:05:49,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:05:49,554] [INFO] Task started: Prodigal
[2023-06-19 10:05:49,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg06a49158-c191-4218-8735-779eb06cc349/GCA_018367515.1_ASM1836751v1_genomic.fna.gz | prodigal -d GCA_018367515.1_ASM1836751v1_genomic.fna/cds.fna -a GCA_018367515.1_ASM1836751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:05:54,347] [INFO] Task succeeded: Prodigal
[2023-06-19 10:05:54,347] [INFO] Task started: HMMsearch
[2023-06-19 10:05:54,348] [INFO] Running command: hmmsearch --tblout GCA_018367515.1_ASM1836751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/reference_markers.hmm GCA_018367515.1_ASM1836751v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:05:54,600] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:05:54,602] [INFO] Found 6/6 markers.
[2023-06-19 10:05:54,625] [INFO] Query marker FASTA was written to GCA_018367515.1_ASM1836751v1_genomic.fna/markers.fasta
[2023-06-19 10:05:54,625] [INFO] Task started: Blastn
[2023-06-19 10:05:54,626] [INFO] Running command: blastn -query GCA_018367515.1_ASM1836751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/reference_markers.fasta -out GCA_018367515.1_ASM1836751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:05:55,257] [INFO] Task succeeded: Blastn
[2023-06-19 10:05:55,260] [INFO] Selected 13 target genomes.
[2023-06-19 10:05:55,261] [INFO] Target genome list was writen to GCA_018367515.1_ASM1836751v1_genomic.fna/target_genomes.txt
[2023-06-19 10:05:55,263] [INFO] Task started: fastANI
[2023-06-19 10:05:55,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg06a49158-c191-4218-8735-779eb06cc349/GCA_018367515.1_ASM1836751v1_genomic.fna.gz --refList GCA_018367515.1_ASM1836751v1_genomic.fna/target_genomes.txt --output GCA_018367515.1_ASM1836751v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:06:00,579] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:00,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:06:00,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:06:00,591] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:06:00,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:06:00,592] [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 salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	89.0773	565	671	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	89.0577	562	671	95	below_threshold
Streptococcus salivarius	strain=NCTC8618	GCA_900636435.1	1304	1304	suspected-type	True	89.0457	563	671	95	below_threshold
Streptococcus salivarius	strain=ATCC 7073	GCA_900143035.1	1304	1304	suspected-type	True	89.017	565	671	95	below_threshold
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	88.5687	513	671	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	87.7238	468	671	95	below_threshold
Streptococcus thermophilus	strain=ATCC 19258	GCA_004354505.1	1308	1308	type	True	87.7202	472	671	95	below_threshold
Streptococcus thermophilus	strain=ATCC 19258	GCA_010120595.1	1308	1308	type	True	87.6785	490	671	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.6915	125	671	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	79.4535	128	671	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.3933	115	671	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.5257	85	671	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	77.6391	66	671	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:06:00,595] [INFO] DFAST Taxonomy check result was written to GCA_018367515.1_ASM1836751v1_genomic.fna/tc_result.tsv
[2023-06-19 10:06:00,596] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:06:00,597] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:06:00,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/checkm_data
[2023-06-19 10:06:00,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:06:00,626] [INFO] Task started: CheckM
[2023-06-19 10:06:00,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018367515.1_ASM1836751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018367515.1_ASM1836751v1_genomic.fna/checkm_input GCA_018367515.1_ASM1836751v1_genomic.fna/checkm_result
[2023-06-19 10:06:22,404] [INFO] Task succeeded: CheckM
[2023-06-19 10:06:22,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:06:22,433] [INFO] ===== Completeness check finished =====
[2023-06-19 10:06:22,434] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:06:22,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018367515.1_ASM1836751v1_genomic.fna/markers.fasta)
[2023-06-19 10:06:22,435] [INFO] Task started: Blastn
[2023-06-19 10:06:22,435] [INFO] Running command: blastn -query GCA_018367515.1_ASM1836751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ee7a75-b681-43d0-b81c-f9f5f1388e55/dqc_reference/reference_markers_gtdb.fasta -out GCA_018367515.1_ASM1836751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:23,256] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:23,263] [INFO] Selected 6 target genomes.
[2023-06-19 10:06:23,263] [INFO] Target genome list was writen to GCA_018367515.1_ASM1836751v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:06:23,267] [INFO] Task started: fastANI
[2023-06-19 10:06:23,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg06a49158-c191-4218-8735-779eb06cc349/GCA_018367515.1_ASM1836751v1_genomic.fna.gz --refList GCA_018367515.1_ASM1836751v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018367515.1_ASM1836751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:06:26,429] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:26,440] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:06:26,441] [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_010604095.1	s__Streptococcus sp000187445	96.5598	587	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	conclusive
GCF_009738225.1	s__Streptococcus sp001556435	89.5329	583	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCF_000785515.1	s__Streptococcus salivarius	89.1007	560	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	-
GCF_000188295.1	s__Streptococcus vestibularis	88.5962	512	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.03	95.83	0.91	0.87	14	-
GCA_003521145.1	s__Streptococcus sp003521145	88.0874	414	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010120595.1	s__Streptococcus thermophilus	87.6785	490	671	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	-
--------------------------------------------------------------------------------
[2023-06-19 10:06:26,458] [INFO] GTDB search result was written to GCA_018367515.1_ASM1836751v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:06:26,459] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:06:26,464] [INFO] DFAST_QC result json was written to GCA_018367515.1_ASM1836751v1_genomic.fna/dqc_result.json
[2023-06-19 10:06:26,464] [INFO] DFAST_QC completed!
[2023-06-19 10:06:26,465] [INFO] Total running time: 0h0m39s