[2024-01-24 13:58:25,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference
[2024-01-24 13:58:26,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,978] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb83c6a-9cd5-446e-8d8c-680e0a530e6a/GCF_900459295.1_42197_F02_genomic.fna.gz | prodigal -d GCF_900459295.1_42197_F02_genomic.fna/cds.fna -a GCF_900459295.1_42197_F02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:31,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:31,255] [INFO] Task started: HMMsearch
[2024-01-24 13:58:31,255] [INFO] Running command: hmmsearch --tblout GCF_900459295.1_42197_F02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/reference_markers.hmm GCF_900459295.1_42197_F02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:31,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:31,474] [INFO] Found 6/6 markers.
[2024-01-24 13:58:31,508] [INFO] Query marker FASTA was written to GCF_900459295.1_42197_F02_genomic.fna/markers.fasta
[2024-01-24 13:58:31,509] [INFO] Task started: Blastn
[2024-01-24 13:58:31,509] [INFO] Running command: blastn -query GCF_900459295.1_42197_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/reference_markers.fasta -out GCF_900459295.1_42197_F02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:32,177] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:32,181] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:32,181] [INFO] Target genome list was writen to GCF_900459295.1_42197_F02_genomic.fna/target_genomes.txt
[2024-01-24 13:58:32,246] [INFO] Task started: fastANI
[2024-01-24 13:58:32,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb83c6a-9cd5-446e-8d8c-680e0a530e6a/GCF_900459295.1_42197_F02_genomic.fna.gz --refList GCF_900459295.1_42197_F02_genomic.fna/target_genomes.txt --output GCF_900459295.1_42197_F02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,636] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,646] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:38,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:38,647] [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 equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	100.0	597	600	95	conclusive
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	99.8861	574	600	95	conclusive
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	88.5547	462	600	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	88.4914	467	600	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	88.4854	472	600	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	87.4981	466	600	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	87.4248	469	600	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	87.3226	456	600	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	86.7838	485	600	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.8347	93	600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,649] [INFO] DFAST Taxonomy check result was written to GCF_900459295.1_42197_F02_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/checkm_data
[2024-01-24 13:58:38,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,691] [INFO] Task started: CheckM
[2024-01-24 13:58:38,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459295.1_42197_F02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459295.1_42197_F02_genomic.fna/checkm_input GCF_900459295.1_42197_F02_genomic.fna/checkm_result
[2024-01-24 13:59:00,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:00,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:00,205] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:00,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:00,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459295.1_42197_F02_genomic.fna/markers.fasta)
[2024-01-24 13:59:00,207] [INFO] Task started: Blastn
[2024-01-24 13:59:00,207] [INFO] Running command: blastn -query GCF_900459295.1_42197_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb71ef35c-691e-4e1b-a455-bc7679c8d8cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459295.1_42197_F02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:00,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:00,976] [INFO] Selected 7 target genomes.
[2024-01-24 13:59:00,977] [INFO] Target genome list was writen to GCF_900459295.1_42197_F02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:00,982] [INFO] Task started: fastANI
[2024-01-24 13:59:00,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb83c6a-9cd5-446e-8d8c-680e0a530e6a/GCF_900459295.1_42197_F02_genomic.fna.gz --refList GCF_900459295.1_42197_F02_genomic.fna/target_genomes_gtdb.txt --output GCF_900459295.1_42197_F02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:04,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:04,209] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:04,210] [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_000187265.1	s__Streptococcus equinus	99.8861	574	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	conclusive
GCF_900475675.1	s__Streptococcus lutetiensis	88.5422	462	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_000154985.1	s__Streptococcus infantarius	87.3234	456	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900101445.1	s__Streptococcus equinus_B	86.8416	478	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_016461705.1	s__Streptococcus vicugnae	86.7838	485	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_900104225.1	s__Streptococcus equinus_D	86.556	484	600	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,211] [INFO] GTDB search result was written to GCF_900459295.1_42197_F02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:04,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:04,215] [INFO] DFAST_QC result json was written to GCF_900459295.1_42197_F02_genomic.fna/dqc_result.json
[2024-01-24 13:59:04,215] [INFO] DFAST_QC completed!
[2024-01-24 13:59:04,215] [INFO] Total running time: 0h0m38s