[2024-01-24 12:31:21,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference
[2024-01-24 12:31:22,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,523] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b0a0d2-7833-4323-94f9-2877d760d7df/GCF_004792515.1_ASM479251v1_genomic.fna.gz | prodigal -d GCF_004792515.1_ASM479251v1_genomic.fna/cds.fna -a GCF_004792515.1_ASM479251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:26,467] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:26,467] [INFO] Task started: HMMsearch
[2024-01-24 12:31:26,467] [INFO] Running command: hmmsearch --tblout GCF_004792515.1_ASM479251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/reference_markers.hmm GCF_004792515.1_ASM479251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:26,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:26,659] [INFO] Found 6/6 markers.
[2024-01-24 12:31:26,679] [INFO] Query marker FASTA was written to GCF_004792515.1_ASM479251v1_genomic.fna/markers.fasta
[2024-01-24 12:31:26,679] [INFO] Task started: Blastn
[2024-01-24 12:31:26,679] [INFO] Running command: blastn -query GCF_004792515.1_ASM479251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/reference_markers.fasta -out GCF_004792515.1_ASM479251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:27,300] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:27,304] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:27,305] [INFO] Target genome list was writen to GCF_004792515.1_ASM479251v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:27,314] [INFO] Task started: fastANI
[2024-01-24 12:31:27,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b0a0d2-7833-4323-94f9-2877d760d7df/GCF_004792515.1_ASM479251v1_genomic.fna.gz --refList GCF_004792515.1_ASM479251v1_genomic.fna/target_genomes.txt --output GCF_004792515.1_ASM479251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:36,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:36,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:36,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:37,000] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:37,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:37,001] [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
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	100.0	690	690	95	conclusive
Vagococcus zengguangii	strain=MN-17	GCA_005145005.1	2571750	2571750	type	True	83.0549	417	690	95	below_threshold
Vagococcus hydrophili	strain=HDW17B	GCA_011304195.1	2714947	2714947	type	True	79.7086	104	690	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	79.6062	86	690	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	79.1669	105	690	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	78.9459	91	690	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	78.3655	90	690	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	78.2732	88	690	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	77.8844	108	690	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	77.8196	104	690	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	77.7942	97	690	95	below_threshold
Enterococcus haemoperoxidus	strain=DSM 15920	GCA_001885985.1	155618	155618	type	True	77.6311	84	690	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.4751	56	690	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	77.4172	69	690	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.3569	74	690	95	below_threshold
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	77.0596	74	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:37,003] [INFO] DFAST Taxonomy check result was written to GCF_004792515.1_ASM479251v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:37,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:37,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:37,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/checkm_data
[2024-01-24 12:31:37,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:37,030] [INFO] Task started: CheckM
[2024-01-24 12:31:37,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004792515.1_ASM479251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004792515.1_ASM479251v1_genomic.fna/checkm_input GCF_004792515.1_ASM479251v1_genomic.fna/checkm_result
[2024-01-24 12:31:55,274] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:55,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,293] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:55,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:55,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004792515.1_ASM479251v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:55,294] [INFO] Task started: Blastn
[2024-01-24 12:31:55,294] [INFO] Running command: blastn -query GCF_004792515.1_ASM479251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaf419b2-a00f-4bd0-a01d-b2b817dc588e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004792515.1_ASM479251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:56,002] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:56,006] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:56,006] [INFO] Target genome list was writen to GCF_004792515.1_ASM479251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:56,018] [INFO] Task started: fastANI
[2024-01-24 12:31:56,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b0a0d2-7833-4323-94f9-2877d760d7df/GCF_004792515.1_ASM479251v1_genomic.fna.gz --refList GCF_004792515.1_ASM479251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004792515.1_ASM479251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:06,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:06,068] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:06,068] [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_004792515.1	s__Vagococcus_A sp004792515	100.0	690	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_005145005.1	s__Vagococcus_A zengguangii	83.0014	415	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	99.48	99.48	0.96	0.96	2	-
GCF_003950315.1	s__Vagococcus bubulae	79.668	85	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303955.1	s__Vagococcus_D coleopterorum	79.5542	98	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011304195.1	s__Vagococcus hydrophili	79.4125	102	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000392875.1	s__Enterococcus faecalis	79.2901	94	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	-
GCF_014397115.1	s__Vagococcus carniphilus	79.2647	107	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009933175.1	s__Enterococcus_B sp009933175	78.9125	74	690	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_000407165.1	s__Enterococcus haemoperoxidus	78.2732	88	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_003462485.1	s__Vagococcus sp003462485	78.0276	88	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004795745.1	s__Vagococcus silagei	77.9647	98	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337315.1	s__Vagococcus fluvialis	77.9159	107	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	77.8784	94	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	77.7942	97	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	98.18	98.18	0.88	0.88	2	-
GCF_017316125.1	s__Enterococcus_B sp017316125	77.7548	65	690	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_001730315.1	s__Enterococcus ureilyticus	77.7009	71	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_014635985.1	s__Enterococcus_I alcedinis	77.3966	73	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016909125.1	s__Enterococcus_I lemanii	77.319	71	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.21	98.21	0.88	0.88	2	-
GCF_001742285.1	s__Enterococcus rivorum	77.0596	74	690	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:06,070] [INFO] GTDB search result was written to GCF_004792515.1_ASM479251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:06,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:06,075] [INFO] DFAST_QC result json was written to GCF_004792515.1_ASM479251v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:06,076] [INFO] DFAST_QC completed!
[2024-01-24 12:32:06,076] [INFO] Total running time: 0h0m45s