[2024-01-24 15:10:20,275] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,277] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference
[2024-01-24 15:10:23,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:23,845] [INFO] Task started: Prodigal
[2024-01-24 15:10:23,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg325b5b6b-5c2e-4f9d-80c2-7fa81289f175/GCF_900104595.1_PRJEB16349_genomic.fna.gz | prodigal -d GCF_900104595.1_PRJEB16349_genomic.fna/cds.fna -a GCF_900104595.1_PRJEB16349_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:28,633] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:28,633] [INFO] Task started: HMMsearch
[2024-01-24 15:10:28,634] [INFO] Running command: hmmsearch --tblout GCF_900104595.1_PRJEB16349_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/reference_markers.hmm GCF_900104595.1_PRJEB16349_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:28,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:28,853] [INFO] Found 6/6 markers.
[2024-01-24 15:10:28,887] [INFO] Query marker FASTA was written to GCF_900104595.1_PRJEB16349_genomic.fna/markers.fasta
[2024-01-24 15:10:28,887] [INFO] Task started: Blastn
[2024-01-24 15:10:28,887] [INFO] Running command: blastn -query GCF_900104595.1_PRJEB16349_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/reference_markers.fasta -out GCF_900104595.1_PRJEB16349_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:30,414] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:30,417] [INFO] Selected 25 target genomes.
[2024-01-24 15:10:30,418] [INFO] Target genome list was writen to GCF_900104595.1_PRJEB16349_genomic.fna/target_genomes.txt
[2024-01-24 15:10:30,580] [INFO] Task started: fastANI
[2024-01-24 15:10:30,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b5b6b-5c2e-4f9d-80c2-7fa81289f175/GCF_900104595.1_PRJEB16349_genomic.fna.gz --refList GCF_900104595.1_PRJEB16349_genomic.fna/target_genomes.txt --output GCF_900104595.1_PRJEB16349_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:43,860] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:43,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:43,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:43,872] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:43,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:43,872] [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 timonensis	strain=Marseille-P2817	GCA_900104595.1	1852364	1852364	type	True	100.0	705	706	95	conclusive
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	80.0538	89	706	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	78.2819	55	706	95	below_threshold
Enterococcus pallens	strain=ATCC BAA-351	GCA_000393975.1	160454	160454	type	True	78.1959	62	706	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	78.17	66	706	95	below_threshold
Enterococcus nangangensis	strain=94-2	GCA_005405245.1	2559926	2559926	type	True	78.1134	136	706	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	77.7936	71	706	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	77.0056	56	706	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	76.9616	63	706	95	below_threshold
Enterococcus haemoperoxidus	strain=DSM 15920	GCA_001885985.1	155618	155618	type	True	76.9248	66	706	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	76.7418	55	706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:43,874] [INFO] DFAST Taxonomy check result was written to GCF_900104595.1_PRJEB16349_genomic.fna/tc_result.tsv
[2024-01-24 15:10:43,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:43,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:43,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/checkm_data
[2024-01-24 15:10:43,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:43,900] [INFO] Task started: CheckM
[2024-01-24 15:10:43,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104595.1_PRJEB16349_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104595.1_PRJEB16349_genomic.fna/checkm_input GCF_900104595.1_PRJEB16349_genomic.fna/checkm_result
[2024-01-24 15:11:05,237] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:05,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:05,256] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:05,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:05,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104595.1_PRJEB16349_genomic.fna/markers.fasta)
[2024-01-24 15:11:05,257] [INFO] Task started: Blastn
[2024-01-24 15:11:05,257] [INFO] Running command: blastn -query GCF_900104595.1_PRJEB16349_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f98e859-5d9b-41f9-ac51-c2d78485beb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104595.1_PRJEB16349_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,132] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,136] [INFO] Selected 25 target genomes.
[2024-01-24 15:11:06,136] [INFO] Target genome list was writen to GCF_900104595.1_PRJEB16349_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:06,177] [INFO] Task started: fastANI
[2024-01-24 15:11:06,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg325b5b6b-5c2e-4f9d-80c2-7fa81289f175/GCF_900104595.1_PRJEB16349_genomic.fna.gz --refList GCF_900104595.1_PRJEB16349_genomic.fna/target_genomes_gtdb.txt --output GCF_900104595.1_PRJEB16349_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:17,958] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:17,986] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:17,986] [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_900104595.1	s__Enterococcus_J timonensis	100.0	705	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011397115.1	s__Enterococcus_C saigonensis	79.713	88	706	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_002140175.1	s__Enterococcus_B sp002140175	79.0478	52	706	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_005405265.1	s__Enterococcus_C songbeiensis	78.7813	71	706	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_005405245.1	s__Enterococcus_J nangangensis	78.1134	136	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115705.1	s__Tetragenococcus pullicola	77.8518	55	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	77.7178	71	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001885735.1	s__Enterococcus_C canintestini	77.5291	69	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
GCF_017315945.1	s__Enterococcus_B sp017315945	77.4772	68	706	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	77.1751	70	706	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_017377655.1	s__Enterococcus_A sp017377655	77.1708	56	706	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	77.0276	57	706	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_017426705.1	s__Enterococcus_F sp017426705	77.0241	54	706	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_007990225.1	s__Enterococcus_B villorum	77.0056	56	706	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_001886195.1	s__Enterococcus_B ratti	76.7387	56	706	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 15:11:17,988] [INFO] GTDB search result was written to GCF_900104595.1_PRJEB16349_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:17,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:17,992] [INFO] DFAST_QC result json was written to GCF_900104595.1_PRJEB16349_genomic.fna/dqc_result.json
[2024-01-24 15:11:17,992] [INFO] DFAST_QC completed!
[2024-01-24 15:11:17,993] [INFO] Total running time: 0h0m58s