[2024-01-24 13:49:00,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,294] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,294] [INFO] DQC Reference Directory: /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference
[2024-01-24 13:49:01,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,638] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg9112f324-6e67-4cd0-9406-3e7412dede8b/GCF_002197645.1_ASM219764v1_genomic.fna.gz | prodigal -d GCF_002197645.1_ASM219764v1_genomic.fna/cds.fna -a GCF_002197645.1_ASM219764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:10,503] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:10,503] [INFO] Task started: HMMsearch
[2024-01-24 13:49:10,503] [INFO] Running command: hmmsearch --tblout GCF_002197645.1_ASM219764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/reference_markers.hmm GCF_002197645.1_ASM219764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:10,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:10,809] [INFO] Found 6/6 markers.
[2024-01-24 13:49:10,859] [INFO] Query marker FASTA was written to GCF_002197645.1_ASM219764v1_genomic.fna/markers.fasta
[2024-01-24 13:49:10,859] [INFO] Task started: Blastn
[2024-01-24 13:49:10,860] [INFO] Running command: blastn -query GCF_002197645.1_ASM219764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/reference_markers.fasta -out GCF_002197645.1_ASM219764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:11,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:11,459] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:11,459] [INFO] Target genome list was writen to GCF_002197645.1_ASM219764v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:11,486] [INFO] Task started: fastANI
[2024-01-24 13:49:11,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg9112f324-6e67-4cd0-9406-3e7412dede8b/GCF_002197645.1_ASM219764v1_genomic.fna.gz --refList GCF_002197645.1_ASM219764v1_genomic.fna/target_genomes.txt --output GCF_002197645.1_ASM219764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:23,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:23,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:23,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:23,016] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:23,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:23,017] [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 wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	100.0	1363	1383	95	conclusive
Enterococcus wangshanyuanii	strain=CGMCC 1.15942	GCA_014644255.1	2005703	2005703	type	True	99.9826	1295	1383	95	conclusive
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	82.2015	783	1383	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	82.1858	799	1383	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	80.6992	594	1383	95	below_threshold
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	80.6171	585	1383	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	80.5785	555	1383	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	80.5687	581	1383	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	80.5596	577	1383	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	80.4334	608	1383	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	80.405	645	1383	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.7108	211	1383	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.6474	131	1383	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.6265	127	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:23,018] [INFO] DFAST Taxonomy check result was written to GCF_002197645.1_ASM219764v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:23,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:23,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:23,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/checkm_data
[2024-01-24 13:49:23,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:23,060] [INFO] Task started: CheckM
[2024-01-24 13:49:23,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002197645.1_ASM219764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002197645.1_ASM219764v1_genomic.fna/checkm_input GCF_002197645.1_ASM219764v1_genomic.fna/checkm_result
[2024-01-24 13:49:55,276] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:55,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,301] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:55,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:55,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002197645.1_ASM219764v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:55,302] [INFO] Task started: Blastn
[2024-01-24 13:49:55,302] [INFO] Running command: blastn -query GCF_002197645.1_ASM219764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc80da2c5-85b2-4fcf-b8ef-890e34d325ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_002197645.1_ASM219764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:56,117] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:56,122] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:56,122] [INFO] Target genome list was writen to GCF_002197645.1_ASM219764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:56,196] [INFO] Task started: fastANI
[2024-01-24 13:49:56,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg9112f324-6e67-4cd0-9406-3e7412dede8b/GCF_002197645.1_ASM219764v1_genomic.fna.gz --refList GCF_002197645.1_ASM219764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002197645.1_ASM219764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:05,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,486] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:05,487] [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_002197645.1	s__Enterococcus wangshanyuanii	100.0	1366	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002174455.1	s__Enterococcus sp002174455	91.0781	1015	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.86	99.86	0.99	0.99	2	-
GCF_001730305.1	s__Enterococcus termitis	82.1926	798	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017377505.1	s__Enterococcus sp017377505	80.7285	580	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	80.675	598	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000407145.1	s__Enterococcus caccae	80.5846	576	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001465345.1	s__Enterococcus rotai	80.5792	580	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730295.1	s__Enterococcus plantarum	80.571	555	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_002148425.1	s__Enterococcus sp002148425	80.4911	623	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_000633635.1	s__Enterococcus crotali	80.4127	646	1383	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCA_001465115.1	s__Enterococcus silesiacus	80.334	624	1383	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 13:50:05,488] [INFO] GTDB search result was written to GCF_002197645.1_ASM219764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:05,489] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:05,492] [INFO] DFAST_QC result json was written to GCF_002197645.1_ASM219764v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:05,493] [INFO] DFAST_QC completed!
[2024-01-24 13:50:05,493] [INFO] Total running time: 0h1m5s