[2024-01-24 12:06:21,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:21,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:21,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference
[2024-01-24 12:06:22,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:22,756] [INFO] Task started: Prodigal
[2024-01-24 12:06:22,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b34c58a-fb7d-4130-b514-cb2c46b9933d/GCF_007989705.1_ASM798970v1_genomic.fna.gz | prodigal -d GCF_007989705.1_ASM798970v1_genomic.fna/cds.fna -a GCF_007989705.1_ASM798970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,598] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,598] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,599] [INFO] Running command: hmmsearch --tblout GCF_007989705.1_ASM798970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/reference_markers.hmm GCF_007989705.1_ASM798970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,848] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,882] [INFO] Query marker FASTA was written to GCF_007989705.1_ASM798970v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,883] [INFO] Task started: Blastn
[2024-01-24 12:06:28,883] [INFO] Running command: blastn -query GCF_007989705.1_ASM798970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/reference_markers.fasta -out GCF_007989705.1_ASM798970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,484] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:29,485] [INFO] Target genome list was writen to GCF_007989705.1_ASM798970v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,509] [INFO] Task started: fastANI
[2024-01-24 12:06:29,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b34c58a-fb7d-4130-b514-cb2c46b9933d/GCF_007989705.1_ASM798970v1_genomic.fna.gz --refList GCF_007989705.1_ASM798970v1_genomic.fna/target_genomes.txt --output GCF_007989705.1_ASM798970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:39,559] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:39,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:39,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:39,573] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:39,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:39,574] [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 thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	100.0	910	910	95	conclusive
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	99.9847	893	910	95	conclusive
Enterococcus durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	79.873	325	910	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	79.761	311	910	95	below_threshold
Enterococcus faecium	strain=NCTC7171	GCA_900447735.1	1352	1352	type	True	79.7001	353	910	95	below_threshold
Enterococcus lactis	strain=LMG 25958	GCA_015904215.1	357441	357441	type	True	79.699	339	910	95	below_threshold
Enterococcus faecium	strain=NBRC 100486	GCA_001544255.1	1352	1352	type	True	79.4242	341	910	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	79.3482	323	910	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	79.343	324	910	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	79.3108	333	910	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	79.2546	344	910	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	79.0953	315	910	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.2631	178	910	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	77.8361	155	910	95	below_threshold
Enterococcus quebecensis	strain=LMG 26306	GCA_001730365.1	903983	903983	type	True	77.6105	144	910	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	77.5453	140	910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:39,575] [INFO] DFAST Taxonomy check result was written to GCF_007989705.1_ASM798970v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:39,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:39,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:39,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/checkm_data
[2024-01-24 12:06:39,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:39,607] [INFO] Task started: CheckM
[2024-01-24 12:06:39,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989705.1_ASM798970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989705.1_ASM798970v1_genomic.fna/checkm_input GCF_007989705.1_ASM798970v1_genomic.fna/checkm_result
[2024-01-24 12:07:03,237] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:03,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:03,254] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:03,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:03,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989705.1_ASM798970v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:03,255] [INFO] Task started: Blastn
[2024-01-24 12:07:03,255] [INFO] Running command: blastn -query GCF_007989705.1_ASM798970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320aad6b-4554-4eee-b274-9349fd9280b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989705.1_ASM798970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:04,049] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:04,054] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:04,054] [INFO] Target genome list was writen to GCF_007989705.1_ASM798970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:04,066] [INFO] Task started: fastANI
[2024-01-24 12:07:04,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b34c58a-fb7d-4130-b514-cb2c46b9933d/GCF_007989705.1_ASM798970v1_genomic.fna.gz --refList GCF_007989705.1_ASM798970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989705.1_ASM798970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:11,664] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:11,679] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:11,680] [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_001886265.1	s__Enterococcus_B thailandicus	99.9847	893	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	conclusive
GCF_017315945.1	s__Enterococcus_B sp017315945	91.483	733	910	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_017316125.1	s__Enterococcus_B sp017316125	90.5659	712	910	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_001544215.1	s__Enterococcus_B durans	79.7893	313	910	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_015751045.1	s__Enterococcus_B lactis	79.6347	346	910	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_002947535.1	s__Enterococcus_B mundtii_B	79.3757	305	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	97.82	97.77	0.91	0.90	3	-
GCA_015680865.1	s__Enterococcus_B lacertideformus	79.3311	282	910	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	79.3305	311	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.33	99.33	0.96	0.96	2	-
GCA_000271405.2	s__Enterococcus_B hirae	79.3108	333	910	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_017316305.1	s__Enterococcus_B sp017316305	79.1126	290	910	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_007990225.1	s__Enterococcus_B villorum	79.0805	316	910	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_009933335.1	s__Enterococcus_F sp009933335	78.1559	149	910	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_001730365.1	s__Enterococcus quebecensis	77.6105	144	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:11,681] [INFO] GTDB search result was written to GCF_007989705.1_ASM798970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:11,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:11,688] [INFO] DFAST_QC result json was written to GCF_007989705.1_ASM798970v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:11,689] [INFO] DFAST_QC completed!
[2024-01-24 12:07:11,689] [INFO] Total running time: 0h0m50s