[2024-01-24 13:37:25,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference
[2024-01-24 13:37:26,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:26,622] [INFO] Task started: Prodigal
[2024-01-24 13:37:26,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg53fa4d0f-5288-455c-81e0-545328ec4b03/GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna.gz | prodigal -d GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/cds.fna -a GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:33,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:33,059] [INFO] Task started: HMMsearch
[2024-01-24 13:37:33,059] [INFO] Running command: hmmsearch --tblout GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/reference_markers.hmm GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:33,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:33,372] [INFO] Found 6/6 markers.
[2024-01-24 13:37:33,398] [INFO] Query marker FASTA was written to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/markers.fasta
[2024-01-24 13:37:33,398] [INFO] Task started: Blastn
[2024-01-24 13:37:33,398] [INFO] Running command: blastn -query GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/reference_markers.fasta -out GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,036] [INFO] Selected 9 target genomes.
[2024-01-24 13:37:34,036] [INFO] Target genome list was writen to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:34,044] [INFO] Task started: fastANI
[2024-01-24 13:37:34,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg53fa4d0f-5288-455c-81e0-545328ec4b03/GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna.gz --refList GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/target_genomes.txt --output GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:40,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:40,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:40,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:40,066] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:37:40,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:40,066] [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_000407425.1	1354	1354	type	True	100.0	958	958	95	conclusive
Enterococcus hirae	strain=FDAARGOS_1123	GCA_016766815.1	1354	1354	type	True	99.9978	957	958	95	conclusive
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	99.9781	941	958	95	conclusive
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	99.9772	950	958	95	conclusive
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	99.9131	912	958	95	conclusive
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	80.1903	385	958	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.7476	111	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:40,068] [INFO] DFAST Taxonomy check result was written to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:40,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:40,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:40,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/checkm_data
[2024-01-24 13:37:40,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:40,123] [INFO] Task started: CheckM
[2024-01-24 13:37:40,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/checkm_input GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/checkm_result
[2024-01-24 13:38:07,261] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:07,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:07,285] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:07,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:07,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/markers.fasta)
[2024-01-24 13:38:07,287] [INFO] Task started: Blastn
[2024-01-24 13:38:07,287] [INFO] Running command: blastn -query GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1678ed0d-5206-468f-b5d7-7761d2a521fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:08,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:08,104] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:08,104] [INFO] Target genome list was writen to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:08,116] [INFO] Task started: fastANI
[2024-01-24 13:38:08,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg53fa4d0f-5288-455c-81e0-545328ec4b03/GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna.gz --refList GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:15,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:15,090] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:15,090] [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	99.9781	941	958	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	81.9989	504	958	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	81.8889	571	958	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	81.205	465	958	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	80.8898	444	958	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_002140175.1	s__Enterococcus_B sp002140175	80.067	363	958	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_011038845.1	s__Enterococcus_B sp011038845	80.0137	378	958	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_001544255.1	s__Enterococcus_B faecium	79.9203	383	958	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_002813755.1	s__Enterococcus_B mundtii	79.77	390	958	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_017316305.1	s__Enterococcus_B sp017316305	79.6951	357	958	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_017316125.1	s__Enterococcus_B sp017316125	79.4787	324	958	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 13:38:15,092] [INFO] GTDB search result was written to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:15,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:15,096] [INFO] DFAST_QC result json was written to GCF_000407425.1_Ente_hira_ATCC8043_V2_genomic.fna/dqc_result.json
[2024-01-24 13:38:15,096] [INFO] DFAST_QC completed!
[2024-01-24 13:38:15,096] [INFO] Total running time: 0h0m50s