[2024-01-24 13:36:45,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference
[2024-01-24 13:36:46,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,369] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg91a79c3a-808b-48b4-9367-5919f017997e/GCF_000271405.2_ASM27140v2_genomic.fna.gz | prodigal -d GCF_000271405.2_ASM27140v2_genomic.fna/cds.fna -a GCF_000271405.2_ASM27140v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:52,425] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:52,425] [INFO] Task started: HMMsearch
[2024-01-24 13:36:52,426] [INFO] Running command: hmmsearch --tblout GCF_000271405.2_ASM27140v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/reference_markers.hmm GCF_000271405.2_ASM27140v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:52,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:52,693] [INFO] Found 6/6 markers.
[2024-01-24 13:36:52,724] [INFO] Query marker FASTA was written to GCF_000271405.2_ASM27140v2_genomic.fna/markers.fasta
[2024-01-24 13:36:52,724] [INFO] Task started: Blastn
[2024-01-24 13:36:52,724] [INFO] Running command: blastn -query GCF_000271405.2_ASM27140v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/reference_markers.fasta -out GCF_000271405.2_ASM27140v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:53,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:53,445] [INFO] Selected 9 target genomes.
[2024-01-24 13:36:53,446] [INFO] Target genome list was writen to GCF_000271405.2_ASM27140v2_genomic.fna/target_genomes.txt
[2024-01-24 13:36:53,460] [INFO] Task started: fastANI
[2024-01-24 13:36:53,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a79c3a-808b-48b4-9367-5919f017997e/GCF_000271405.2_ASM27140v2_genomic.fna.gz --refList GCF_000271405.2_ASM27140v2_genomic.fna/target_genomes.txt --output GCF_000271405.2_ASM27140v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:59,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:59,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:59,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:59,302] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:36:59,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:59,302] [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
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	100.0	951	951	95	conclusive
Enterococcus hirae	strain=FDAARGOS_1123	GCA_016766815.1	1354	1354	type	True	99.9782	948	951	95	conclusive
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	99.9728	942	951	95	conclusive
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	99.9569	941	951	95	conclusive
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	99.9184	895	951	95	conclusive
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	80.0698	380	951	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.4607	119	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:59,303] [INFO] DFAST Taxonomy check result was written to GCF_000271405.2_ASM27140v2_genomic.fna/tc_result.tsv
[2024-01-24 13:36:59,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:59,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:59,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/checkm_data
[2024-01-24 13:36:59,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:59,339] [INFO] Task started: CheckM
[2024-01-24 13:36:59,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000271405.2_ASM27140v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000271405.2_ASM27140v2_genomic.fna/checkm_input GCF_000271405.2_ASM27140v2_genomic.fna/checkm_result
[2024-01-24 13:37:25,535] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:25,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:25,574] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:25,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:25,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000271405.2_ASM27140v2_genomic.fna/markers.fasta)
[2024-01-24 13:37:25,576] [INFO] Task started: Blastn
[2024-01-24 13:37:25,576] [INFO] Running command: blastn -query GCF_000271405.2_ASM27140v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg767610bf-7089-4b56-8635-c1f17f22a8b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000271405.2_ASM27140v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:26,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:26,774] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:26,774] [INFO] Target genome list was writen to GCF_000271405.2_ASM27140v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:26,786] [INFO] Task started: fastANI
[2024-01-24 13:37:26,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a79c3a-808b-48b4-9367-5919f017997e/GCF_000271405.2_ASM27140v2_genomic.fna.gz --refList GCF_000271405.2_ASM27140v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000271405.2_ASM27140v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:35,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,021] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:35,022] [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
GCA_000271405.2	s__Enterococcus_B hirae	100.0	951	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	conclusive
GCA_015680865.1	s__Enterococcus_B lacertideformus	82.1293	503	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990225.1	s__Enterococcus_B villorum	81.9988	562	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
GCF_001544215.1	s__Enterococcus_B durans	81.0627	464	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.77	96.42	0.88	0.77	135	-
GCF_001886195.1	s__Enterococcus_B ratti	80.6306	451	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544255.1	s__Enterococcus_B faecium	80.2334	368	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.30	98.03	0.91	0.72	2177	-
GCF_011038845.1	s__Enterococcus_B sp011038845	80.0315	382	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.61	99.61	0.98	0.98	2	-
GCF_002813755.1	s__Enterococcus_B mundtii	79.953	393	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCF_002140175.1	s__Enterococcus_B sp002140175	79.9084	380	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.33	99.33	0.96	0.96	2	-
GCF_017316125.1	s__Enterococcus_B sp017316125	79.6998	313	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316305.1	s__Enterococcus_B sp017316305	79.49	371	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
GCF_017315945.1	s__Enterococcus_B sp017315945	79.4071	316	951	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,023] [INFO] GTDB search result was written to GCF_000271405.2_ASM27140v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:35,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:35,027] [INFO] DFAST_QC result json was written to GCF_000271405.2_ASM27140v2_genomic.fna/dqc_result.json
[2024-01-24 13:37:35,028] [INFO] DFAST_QC completed!
[2024-01-24 13:37:35,028] [INFO] Total running time: 0h0m50s