[2024-01-24 13:09:50,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:50,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:50,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference
[2024-01-24 13:09:51,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:51,990] [INFO] Task started: Prodigal
[2024-01-24 13:09:51,991] [INFO] Running command: gunzip -c /var/lib/cwl/stgc37fd606-3bf8-4bd4-a1ae-d4b1cf676aa3/GCF_019972875.1_ASM1997287v1_genomic.fna.gz | prodigal -d GCF_019972875.1_ASM1997287v1_genomic.fna/cds.fna -a GCF_019972875.1_ASM1997287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:56,239] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:56,239] [INFO] Task started: HMMsearch
[2024-01-24 13:09:56,239] [INFO] Running command: hmmsearch --tblout GCF_019972875.1_ASM1997287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/reference_markers.hmm GCF_019972875.1_ASM1997287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:56,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:56,478] [INFO] Found 6/6 markers.
[2024-01-24 13:09:56,497] [INFO] Query marker FASTA was written to GCF_019972875.1_ASM1997287v1_genomic.fna/markers.fasta
[2024-01-24 13:09:56,498] [INFO] Task started: Blastn
[2024-01-24 13:09:56,498] [INFO] Running command: blastn -query GCF_019972875.1_ASM1997287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/reference_markers.fasta -out GCF_019972875.1_ASM1997287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:57,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:57,130] [INFO] Selected 11 target genomes.
[2024-01-24 13:09:57,130] [INFO] Target genome list was writen to GCF_019972875.1_ASM1997287v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:57,155] [INFO] Task started: fastANI
[2024-01-24 13:09:57,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgc37fd606-3bf8-4bd4-a1ae-d4b1cf676aa3/GCF_019972875.1_ASM1997287v1_genomic.fna.gz --refList GCF_019972875.1_ASM1997287v1_genomic.fna/target_genomes.txt --output GCF_019972875.1_ASM1997287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:02,445] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:02,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:02,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:02,453] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:02,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:02,453] [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 thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	100.0	631	636	95	conclusive
Streptococcus thermophilus	strain=ATCC 19258	GCA_010120595.1	1308	1308	type	True	99.9933	636	636	95	conclusive
Streptococcus thermophilus	strain=ATCC 19258	GCA_004354505.1	1308	1308	type	True	99.9865	630	636	95	conclusive
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	92.1871	496	636	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	89.0834	481	636	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	89.0643	486	636	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	80.3428	79	636	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.568	65	636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:02,456] [INFO] DFAST Taxonomy check result was written to GCF_019972875.1_ASM1997287v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:02,456] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:02,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:02,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/checkm_data
[2024-01-24 13:10:02,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:02,483] [INFO] Task started: CheckM
[2024-01-24 13:10:02,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019972875.1_ASM1997287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019972875.1_ASM1997287v1_genomic.fna/checkm_input GCF_019972875.1_ASM1997287v1_genomic.fna/checkm_result
[2024-01-24 13:10:23,168] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:23,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:23,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:23,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019972875.1_ASM1997287v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:23,190] [INFO] Task started: Blastn
[2024-01-24 13:10:23,190] [INFO] Running command: blastn -query GCF_019972875.1_ASM1997287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f1cd6e-4241-46a7-bec0-4fdafd6bad20/dqc_reference/reference_markers_gtdb.fasta -out GCF_019972875.1_ASM1997287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:24,068] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:24,072] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:24,073] [INFO] Target genome list was writen to GCF_019972875.1_ASM1997287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:24,078] [INFO] Task started: fastANI
[2024-01-24 13:10:24,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc37fd606-3bf8-4bd4-a1ae-d4b1cf676aa3/GCF_019972875.1_ASM1997287v1_genomic.fna.gz --refList GCF_019972875.1_ASM1997287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019972875.1_ASM1997287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:27,404] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:27,410] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:27,410] [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_010120595.1	s__Streptococcus thermophilus	99.9933	636	636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	conclusive
GCF_000188295.1	s__Streptococcus vestibularis	92.1871	496	636	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	90.228	435	636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009738225.1	s__Streptococcus sp001556435	89.4629	487	636	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	89.0901	480	636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	-
GCF_010604095.1	s__Streptococcus sp000187445	88.0173	467	636	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:27,412] [INFO] GTDB search result was written to GCF_019972875.1_ASM1997287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:27,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:27,421] [INFO] DFAST_QC result json was written to GCF_019972875.1_ASM1997287v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:27,421] [INFO] DFAST_QC completed!
[2024-01-24 13:10:27,421] [INFO] Total running time: 0h0m37s