[2023-06-05 09:25:11,622] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:11,625] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:11,625] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference
[2023-06-05 09:25:13,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:13,161] [INFO] Task started: Prodigal
[2023-06-05 09:25:13,161] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd0290e4-d7d6-450b-ace8-cfeeb2c133b0/GCA_934875685.1_MTG238_bin.34.fa_genomic.fna.gz | prodigal -d GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/cds.fna -a GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:16,692] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:16,693] [INFO] Task started: HMMsearch
[2023-06-05 09:25:16,693] [INFO] Running command: hmmsearch --tblout GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/reference_markers.hmm GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:16,950] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:16,951] [INFO] Found 6/6 markers.
[2023-06-05 09:25:16,988] [INFO] Query marker FASTA was written to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/markers.fasta
[2023-06-05 09:25:16,988] [INFO] Task started: Blastn
[2023-06-05 09:25:16,988] [INFO] Running command: blastn -query GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/reference_markers.fasta -out GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:17,624] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:17,628] [INFO] Selected 11 target genomes.
[2023-06-05 09:25:17,628] [INFO] Target genome list was writen to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/target_genomes.txt
[2023-06-05 09:25:17,633] [INFO] Task started: fastANI
[2023-06-05 09:25:17,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0290e4-d7d6-450b-ace8-cfeeb2c133b0/GCA_934875685.1_MTG238_bin.34.fa_genomic.fna.gz --refList GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/target_genomes.txt --output GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:25:22,699] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:22,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:25:22,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:25:22,709] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2023-06-05 09:25:22,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 09:25:22,709] [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=ATCC 19258	GCA_004354505.1	1308	1308	type	True	98.7177	479	518	95	conclusive
Streptococcus thermophilus	strain=ATCC 19258	GCA_010120595.1	1308	1308	type	True	98.7095	491	518	95	conclusive
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	98.6814	477	518	95	conclusive
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	92.3616	464	518	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	89.0253	468	518	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	88.9904	461	518	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.938	65	518	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.3054	62	518	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:25:22,711] [INFO] DFAST Taxonomy check result was written to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/tc_result.tsv
[2023-06-05 09:25:22,712] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:25:22,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:25:22,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/checkm_data
[2023-06-05 09:25:22,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:25:22,733] [INFO] Task started: CheckM
[2023-06-05 09:25:22,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/checkm_input GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/checkm_result
[2023-06-05 09:25:42,234] [INFO] Task succeeded: CheckM
[2023-06-05 09:25:42,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:25:42,258] [INFO] ===== Completeness check finished =====
[2023-06-05 09:25:42,259] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:25:42,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/markers.fasta)
[2023-06-05 09:25:42,260] [INFO] Task started: Blastn
[2023-06-05 09:25:42,260] [INFO] Running command: blastn -query GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1874e42-3eaf-4d97-9e26-70fbe5e9fdc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:43,145] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:43,148] [INFO] Selected 6 target genomes.
[2023-06-05 09:25:43,149] [INFO] Target genome list was writen to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:25:43,156] [INFO] Task started: fastANI
[2023-06-05 09:25:43,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0290e4-d7d6-450b-ace8-cfeeb2c133b0/GCA_934875685.1_MTG238_bin.34.fa_genomic.fna.gz --refList GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:25:46,020] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:46,034] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:25:46,034] [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	98.7095	491	518	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	92.3616	464	518	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	89.8988	392	518	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	89.5237	460	518	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	88.9904	461	518	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	87.9301	441	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
--------------------------------------------------------------------------------
[2023-06-05 09:25:46,036] [INFO] GTDB search result was written to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 09:25:46,037] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:25:46,040] [INFO] DFAST_QC result json was written to GCA_934875685.1_MTG238_bin.34.fa_genomic.fna/dqc_result.json
[2023-06-05 09:25:46,040] [INFO] DFAST_QC completed!
[2023-06-05 09:25:46,041] [INFO] Total running time: 0h0m34s