[2024-01-24 15:18:32,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:32,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:32,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference
[2024-01-24 15:18:34,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:34,815] [INFO] Task started: Prodigal
[2024-01-24 15:18:34,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg74b82e06-7a48-42e4-b4cc-9dded32defd0/GCF_900447665.1_44927_C01_genomic.fna.gz | prodigal -d GCF_900447665.1_44927_C01_genomic.fna/cds.fna -a GCF_900447665.1_44927_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:43,658] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:43,658] [INFO] Task started: HMMsearch
[2024-01-24 15:18:43,658] [INFO] Running command: hmmsearch --tblout GCF_900447665.1_44927_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/reference_markers.hmm GCF_900447665.1_44927_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:43,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:43,869] [INFO] Found 6/6 markers.
[2024-01-24 15:18:43,901] [INFO] Query marker FASTA was written to GCF_900447665.1_44927_C01_genomic.fna/markers.fasta
[2024-01-24 15:18:43,901] [INFO] Task started: Blastn
[2024-01-24 15:18:43,901] [INFO] Running command: blastn -query GCF_900447665.1_44927_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/reference_markers.fasta -out GCF_900447665.1_44927_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:44,474] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:44,477] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:44,477] [INFO] Target genome list was writen to GCF_900447665.1_44927_C01_genomic.fna/target_genomes.txt
[2024-01-24 15:18:44,498] [INFO] Task started: fastANI
[2024-01-24 15:18:44,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b82e06-7a48-42e4-b4cc-9dded32defd0/GCF_900447665.1_44927_C01_genomic.fna.gz --refList GCF_900447665.1_44927_C01_genomic.fna/target_genomes.txt --output GCF_900447665.1_44927_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:52,158] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:52,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:52,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:52,167] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:18:52,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:52,167] [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 casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	100.0	1183	1184	95	conclusive
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	99.9977	1180	1184	95	conclusive
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	99.9624	1139	1184	95	conclusive
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	99.9429	1123	1184	95	conclusive
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	80.483	410	1184	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	79.8898	124	1184	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	79.5635	133	1184	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	79.522	129	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:52,169] [INFO] DFAST Taxonomy check result was written to GCF_900447665.1_44927_C01_genomic.fna/tc_result.tsv
[2024-01-24 15:18:52,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:52,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:52,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/checkm_data
[2024-01-24 15:18:52,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:52,205] [INFO] Task started: CheckM
[2024-01-24 15:18:52,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447665.1_44927_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447665.1_44927_C01_genomic.fna/checkm_input GCF_900447665.1_44927_C01_genomic.fna/checkm_result
[2024-01-24 15:19:23,227] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:23,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:23,246] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:23,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:23,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447665.1_44927_C01_genomic.fna/markers.fasta)
[2024-01-24 15:19:23,247] [INFO] Task started: Blastn
[2024-01-24 15:19:23,247] [INFO] Running command: blastn -query GCF_900447665.1_44927_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e2d595b-1ade-4a6b-8379-a63352252682/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447665.1_44927_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:23,976] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:23,983] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:23,983] [INFO] Target genome list was writen to GCF_900447665.1_44927_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:23,997] [INFO] Task started: fastANI
[2024-01-24 15:19:23,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b82e06-7a48-42e4-b4cc-9dded32defd0/GCF_900447665.1_44927_C01_genomic.fna.gz --refList GCF_900447665.1_44927_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447665.1_44927_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:31,915] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:31,924] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:31,924] [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_001544095.1	s__Enterococcus_D casseliflavus	99.9624	1139	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	98.00	95.35	0.87	0.83	83	conclusive
GCF_002850555.1	s__Enterococcus_D sp002850555	94.8469	1007	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.34	95.31	0.87	0.74	46	-
GCF_002140915.1	s__Enterococcus_D sp002140915	80.7055	497	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544275.1	s__Enterococcus_D gallinarum	80.629	419	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.60	97.23	0.85	0.80	74	-
GCF_001297065.1	s__Enterococcus_D sp001297065	80.4441	491	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCF_011397115.1	s__Enterococcus_C saigonensis	79.8359	124	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316025.1	s__Enterococcus_C sp017316025	79.3393	118	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009933335.1	s__Enterococcus_F sp009933335	78.8096	144	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544255.1	s__Enterococcus_B faecium	78.7495	141	1184	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_005405265.1	s__Enterococcus_C songbeiensis	77.9996	158	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.82	98.68	0.87	0.87	4	-
GCF_017316305.1	s__Enterococcus_B sp017316305	77.9085	146	1184	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,926] [INFO] GTDB search result was written to GCF_900447665.1_44927_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:31,926] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:31,929] [INFO] DFAST_QC result json was written to GCF_900447665.1_44927_C01_genomic.fna/dqc_result.json
[2024-01-24 15:19:31,929] [INFO] DFAST_QC completed!
[2024-01-24 15:19:31,929] [INFO] Total running time: 0h0m59s