[2024-01-25 17:46:20,791] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,793] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference
[2024-01-25 17:46:21,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,927] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgac0fdea6-8685-4ae1-97cd-7848f616dfbd/GCF_026953455.1_ASM2695345v1_genomic.fna.gz | prodigal -d GCF_026953455.1_ASM2695345v1_genomic.fna/cds.fna -a GCF_026953455.1_ASM2695345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:26,940] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:26,940] [INFO] Task started: HMMsearch
[2024-01-25 17:46:26,940] [INFO] Running command: hmmsearch --tblout GCF_026953455.1_ASM2695345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/reference_markers.hmm GCF_026953455.1_ASM2695345v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:27,137] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:27,138] [INFO] Found 6/6 markers.
[2024-01-25 17:46:27,162] [INFO] Query marker FASTA was written to GCF_026953455.1_ASM2695345v1_genomic.fna/markers.fasta
[2024-01-25 17:46:27,162] [INFO] Task started: Blastn
[2024-01-25 17:46:27,162] [INFO] Running command: blastn -query GCF_026953455.1_ASM2695345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/reference_markers.fasta -out GCF_026953455.1_ASM2695345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:27,720] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:27,724] [INFO] Selected 12 target genomes.
[2024-01-25 17:46:27,724] [INFO] Target genome list was writen to GCF_026953455.1_ASM2695345v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:27,726] [INFO] Task started: fastANI
[2024-01-25 17:46:27,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0fdea6-8685-4ae1-97cd-7848f616dfbd/GCF_026953455.1_ASM2695345v1_genomic.fna.gz --refList GCF_026953455.1_ASM2695345v1_genomic.fna/target_genomes.txt --output GCF_026953455.1_ASM2695345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:35,148] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:35,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:35,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:35,156] [WARNING] Following organisms are indistinguishable with ANI. [Enterococcus faecium(1352), Enterococcus lactis(357441)]
[2024-01-25 17:46:35,156] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:46:35,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:35,156] [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 faecium	strain=NCTC7171	GCA_900447735.1	1352	1352	type	True	99.9917	838	840	95	conclusive
Enterococcus faecium	strain=NBRC 100486	GCA_001544255.1	1352	1352	type	True	99.9606	797	840	95	conclusive
Enterococcus lactis	strain=LMG 25958	GCA_015904215.1	357441	357441	type	True	94.6055	753	840	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	94.5305	744	840	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	81.3036	407	840	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	80.0491	381	840	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	80.0066	381	840	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	79.764	345	840	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	79.5362	361	840	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.8573	96	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:35,157] [INFO] DFAST Taxonomy check result was written to GCF_026953455.1_ASM2695345v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:35,158] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:35,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:35,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/checkm_data
[2024-01-25 17:46:35,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:35,193] [INFO] Task started: CheckM
[2024-01-25 17:46:35,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026953455.1_ASM2695345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026953455.1_ASM2695345v1_genomic.fna/checkm_input GCF_026953455.1_ASM2695345v1_genomic.fna/checkm_result
[2024-01-25 17:46:55,820] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:55,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:55,843] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:55,843] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:55,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026953455.1_ASM2695345v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:55,844] [INFO] Task started: Blastn
[2024-01-25 17:46:55,844] [INFO] Running command: blastn -query GCF_026953455.1_ASM2695345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a57967-e6ab-4959-8a1e-b94e71364b6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026953455.1_ASM2695345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:56,582] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:56,584] [INFO] Selected 12 target genomes.
[2024-01-25 17:46:56,584] [INFO] Target genome list was writen to GCF_026953455.1_ASM2695345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:56,592] [INFO] Task started: fastANI
[2024-01-25 17:46:56,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0fdea6-8685-4ae1-97cd-7848f616dfbd/GCF_026953455.1_ASM2695345v1_genomic.fna.gz --refList GCF_026953455.1_ASM2695345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026953455.1_ASM2695345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:04,702] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:04,710] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:04,710] [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_001544255.1	s__Enterococcus_B faecium	99.9606	797	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.30	98.03	0.91	0.72	2177	conclusive
GCF_015751045.1	s__Enterococcus_B lactis	94.5066	745	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.26	97.66	0.89	0.81	335	-
GCF_011038845.1	s__Enterococcus_B sp011038845	81.5912	517	840	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_001544215.1	s__Enterococcus_B durans	81.2995	407	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.77	96.42	0.88	0.77	135	-
GCA_000271405.2	s__Enterococcus_B hirae	79.992	382	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_002947535.1	s__Enterococcus_B mundtii_B	79.8995	336	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	97.82	97.77	0.91	0.90	3	-
GCF_007990225.1	s__Enterococcus_B villorum	79.777	344	840	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_017315945.1	s__Enterococcus_B sp017315945	79.6465	315	840	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_002813755.1	s__Enterococcus_B mundtii	79.5489	362	840	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_003957375.1	s__Enterococcus_B mundtii_C	79.5007	339	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.247	99.65	99.65	0.94	0.94	2	-
GCF_002140175.1	s__Enterococcus_B sp002140175	79.4742	354	840	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_017316305.1	s__Enterococcus_B sp017316305	79.4686	324	840	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:04,718] [INFO] GTDB search result was written to GCF_026953455.1_ASM2695345v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:04,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:04,723] [INFO] DFAST_QC result json was written to GCF_026953455.1_ASM2695345v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:04,723] [INFO] DFAST_QC completed!
[2024-01-25 17:47:04,723] [INFO] Total running time: 0h0m44s