[2024-01-25 17:44:50,399] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,404] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference
[2024-01-25 17:44:51,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,550] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg03a04abc-de38-4a7d-a0ea-248c5c0a004f/GCF_011397115.1_ASM1139711v1_genomic.fna.gz | prodigal -d GCF_011397115.1_ASM1139711v1_genomic.fna/cds.fna -a GCF_011397115.1_ASM1139711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:56,633] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:56,634] [INFO] Task started: HMMsearch
[2024-01-25 17:44:56,634] [INFO] Running command: hmmsearch --tblout GCF_011397115.1_ASM1139711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/reference_markers.hmm GCF_011397115.1_ASM1139711v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:56,845] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:56,846] [INFO] Found 6/6 markers.
[2024-01-25 17:44:56,869] [INFO] Query marker FASTA was written to GCF_011397115.1_ASM1139711v1_genomic.fna/markers.fasta
[2024-01-25 17:44:56,869] [INFO] Task started: Blastn
[2024-01-25 17:44:56,869] [INFO] Running command: blastn -query GCF_011397115.1_ASM1139711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/reference_markers.fasta -out GCF_011397115.1_ASM1139711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:57,439] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:57,443] [INFO] Selected 14 target genomes.
[2024-01-25 17:44:57,443] [INFO] Target genome list was writen to GCF_011397115.1_ASM1139711v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:57,454] [INFO] Task started: fastANI
[2024-01-25 17:44:57,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a04abc-de38-4a7d-a0ea-248c5c0a004f/GCF_011397115.1_ASM1139711v1_genomic.fna.gz --refList GCF_011397115.1_ASM1139711v1_genomic.fna/target_genomes.txt --output GCF_011397115.1_ASM1139711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:05,109] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:05,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:05,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:05,119] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:05,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:05,120] [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 saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	100.0	944	947	95	conclusive
Enterococcus dispar	strain=ATCC 51266	GCA_000407585.1	44009	44009	type	True	83.2163	632	947	95	below_threshold
Enterococcus dispar	strain=ATCC 51266	GCA_000406945.1	44009	44009	type	True	83.1216	616	947	95	below_threshold
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	82.9626	611	947	95	below_threshold
Enterococcus canintestini	strain=DSM 21207	GCA_001885735.1	317010	317010	type	True	82.6695	557	947	95	below_threshold
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	80.0135	115	947	95	below_threshold
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	79.9587	121	947	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	78.974	110	947	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.7506	138	947	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	78.6447	111	947	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.6145	138	947	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:05,121] [INFO] DFAST Taxonomy check result was written to GCF_011397115.1_ASM1139711v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:05,122] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:05,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:05,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/checkm_data
[2024-01-25 17:45:05,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:05,154] [INFO] Task started: CheckM
[2024-01-25 17:45:05,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011397115.1_ASM1139711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011397115.1_ASM1139711v1_genomic.fna/checkm_input GCF_011397115.1_ASM1139711v1_genomic.fna/checkm_result
[2024-01-25 17:45:25,547] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:25,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:25,591] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:25,591] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:25,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011397115.1_ASM1139711v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:25,591] [INFO] Task started: Blastn
[2024-01-25 17:45:25,591] [INFO] Running command: blastn -query GCF_011397115.1_ASM1139711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa0e5ee0-fab4-4489-9550-66e0e0f42803/dqc_reference/reference_markers_gtdb.fasta -out GCF_011397115.1_ASM1139711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:26,392] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:26,394] [INFO] Selected 12 target genomes.
[2024-01-25 17:45:26,394] [INFO] Target genome list was writen to GCF_011397115.1_ASM1139711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:26,402] [INFO] Task started: fastANI
[2024-01-25 17:45:26,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a04abc-de38-4a7d-a0ea-248c5c0a004f/GCF_011397115.1_ASM1139711v1_genomic.fna.gz --refList GCF_011397115.1_ASM1139711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011397115.1_ASM1139711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:32,938] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:32,945] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:32,946] [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_011397115.1	s__Enterococcus_C saigonensis	100.0	945	947	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017316025.1	s__Enterococcus_C sp017316025	85.1988	702	947	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_000406945.1	s__Enterococcus_C dispar	83.1239	613	947	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	99.61	99.21	0.95	0.90	5	-
GCF_001885735.1	s__Enterococcus_C canintestini	82.6695	557	947	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_005405265.1	s__Enterococcus_C songbeiensis	79.6215	156	947	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_001886265.1	s__Enterococcus_B thailandicus	79.4741	152	947	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_002850555.1	s__Enterococcus_D sp002850555	79.3048	117	947	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_001544095.1	s__Enterococcus_D casseliflavus	78.974	110	947	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_000407285.1	s__Enterococcus_F saccharolyticus	78.099	141	947	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_017316125.1	s__Enterococcus_B sp017316125	77.7976	149	947	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_017426705.1	s__Enterococcus_F sp017426705	77.7581	153	947	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:32,948] [INFO] GTDB search result was written to GCF_011397115.1_ASM1139711v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:32,949] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:32,951] [INFO] DFAST_QC result json was written to GCF_011397115.1_ASM1139711v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:32,951] [INFO] DFAST_QC completed!
[2024-01-25 17:45:32,951] [INFO] Total running time: 0h0m43s