[2024-01-24 13:32:41,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference
[2024-01-24 13:32:42,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,763] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc0e69da-5e06-4a23-bf85-829db7ea0dc3/GCF_005405265.1_ASM540526v1_genomic.fna.gz | prodigal -d GCF_005405265.1_ASM540526v1_genomic.fna/cds.fna -a GCF_005405265.1_ASM540526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:48,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:48,450] [INFO] Task started: HMMsearch
[2024-01-24 13:32:48,450] [INFO] Running command: hmmsearch --tblout GCF_005405265.1_ASM540526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/reference_markers.hmm GCF_005405265.1_ASM540526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:48,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:48,713] [INFO] Found 6/6 markers.
[2024-01-24 13:32:48,740] [INFO] Query marker FASTA was written to GCF_005405265.1_ASM540526v1_genomic.fna/markers.fasta
[2024-01-24 13:32:48,741] [INFO] Task started: Blastn
[2024-01-24 13:32:48,741] [INFO] Running command: blastn -query GCF_005405265.1_ASM540526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/reference_markers.fasta -out GCF_005405265.1_ASM540526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,397] [INFO] Selected 25 target genomes.
[2024-01-24 13:32:49,398] [INFO] Target genome list was writen to GCF_005405265.1_ASM540526v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:49,460] [INFO] Task started: fastANI
[2024-01-24 13:32:49,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc0e69da-5e06-4a23-bf85-829db7ea0dc3/GCF_005405265.1_ASM540526v1_genomic.fna.gz --refList GCF_005405265.1_ASM540526v1_genomic.fna/target_genomes.txt --output GCF_005405265.1_ASM540526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:00,570] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:00,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:00,586] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:00,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:00,587] [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 mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	79.6493	328	738	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	79.4404	147	738	95	below_threshold
Enterococcus durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	78.6494	116	738	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	78.4686	110	738	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	78.1824	135	738	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	78.1453	120	738	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	78.0696	153	738	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	78.0607	121	738	95	below_threshold
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	78.0263	153	738	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	78.0059	133	738	95	below_threshold
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	77.9905	154	738	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	77.9573	152	738	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	77.7828	122	738	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	77.5673	98	738	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	77.455	102	738	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	77.3826	99	738	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.378	100	738	95	below_threshold
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	77.3535	100	738	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	77.233	118	738	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.0106	58	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,588] [INFO] DFAST Taxonomy check result was written to GCF_005405265.1_ASM540526v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:00,589] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:00,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:00,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/checkm_data
[2024-01-24 13:33:00,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:00,615] [INFO] Task started: CheckM
[2024-01-24 13:33:00,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405265.1_ASM540526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405265.1_ASM540526v1_genomic.fna/checkm_input GCF_005405265.1_ASM540526v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,131] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405265.1_ASM540526v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,132] [INFO] Task started: Blastn
[2024-01-24 13:33:25,132] [INFO] Running command: blastn -query GCF_005405265.1_ASM540526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15069ceb-c236-4d89-81f1-cedee252e713/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405265.1_ASM540526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:25,941] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:25,944] [INFO] Selected 23 target genomes.
[2024-01-24 13:33:25,945] [INFO] Target genome list was writen to GCF_005405265.1_ASM540526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:25,968] [INFO] Task started: fastANI
[2024-01-24 13:33:25,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc0e69da-5e06-4a23-bf85-829db7ea0dc3/GCF_005405265.1_ASM540526v1_genomic.fna.gz --refList GCF_005405265.1_ASM540526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405265.1_ASM540526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:37,440] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:37,460] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:37,461] [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_005405265.1	s__Enterococcus_C songbeiensis	100.0	736	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.82	98.68	0.87	0.87	4	conclusive
GCF_900604485.1	s__Enterococcus_C mediterraneensis	79.6582	327	738	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_011397115.1	s__Enterococcus_C saigonensis	79.4624	145	738	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_005405205.1	s__Enterococcus_A pingfangensis	79.1825	105	738	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_017315945.1	s__Enterococcus_B sp017315945	79.1491	135	738	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_011038845.1	s__Enterococcus_B sp011038845	79.0663	105	738	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	78.4372	110	738	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_002140915.1	s__Enterococcus_D sp002140915	78.2519	133	738	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_001885735.1	s__Enterococcus_C canintestini	78.1743	129	738	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_002850555.1	s__Enterococcus_D sp002850555	78.1229	148	738	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_009933135.1	s__Enterococcus_C sp009933135	78.0651	113	738	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_001544095.1	s__Enterococcus_D casseliflavus	78.0463	154	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	98.00	95.35	0.87	0.83	83	-
GCF_001886265.1	s__Enterococcus_B thailandicus	78.0241	133	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.8693	133	738	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_009933175.1	s__Enterococcus_B sp009933175	77.8108	126	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116505.1	s__Enterococcus_I avicola	77.7532	64	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.7383	121	738	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_000407285.1	s__Enterococcus_F saccharolyticus	77.6985	133	738	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_000415185.1	s__Enterococcus_B faecalis_A	77.6366	143	738	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_001730305.1	s__Enterococcus termitis	77.5673	98	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007990225.1	s__Enterococcus_B villorum	77.2091	119	738	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:37,462] [INFO] GTDB search result was written to GCF_005405265.1_ASM540526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:37,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:37,469] [INFO] DFAST_QC result json was written to GCF_005405265.1_ASM540526v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:37,469] [INFO] DFAST_QC completed!
[2024-01-24 13:33:37,469] [INFO] Total running time: 0h0m56s