[2024-01-24 12:06:50,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference
[2024-01-24 12:06:52,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,154] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgc224c3ed-f23b-403c-9f12-e40fa2d49381/GCF_018982785.1_ASM1898278v1_genomic.fna.gz | prodigal -d GCF_018982785.1_ASM1898278v1_genomic.fna/cds.fna -a GCF_018982785.1_ASM1898278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:01,373] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:01,374] [INFO] Task started: HMMsearch
[2024-01-24 12:07:01,374] [INFO] Running command: hmmsearch --tblout GCF_018982785.1_ASM1898278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/reference_markers.hmm GCF_018982785.1_ASM1898278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:01,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:01,646] [INFO] Found 6/6 markers.
[2024-01-24 12:07:01,678] [INFO] Query marker FASTA was written to GCF_018982785.1_ASM1898278v1_genomic.fna/markers.fasta
[2024-01-24 12:07:01,678] [INFO] Task started: Blastn
[2024-01-24 12:07:01,678] [INFO] Running command: blastn -query GCF_018982785.1_ASM1898278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/reference_markers.fasta -out GCF_018982785.1_ASM1898278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:02,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:02,317] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:02,318] [INFO] Target genome list was writen to GCF_018982785.1_ASM1898278v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:02,323] [INFO] Task started: fastANI
[2024-01-24 12:07:02,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgc224c3ed-f23b-403c-9f12-e40fa2d49381/GCF_018982785.1_ASM1898278v1_genomic.fna.gz --refList GCF_018982785.1_ASM1898278v1_genomic.fna/target_genomes.txt --output GCF_018982785.1_ASM1898278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:09,727] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:09,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:09,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:09,738] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:09,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:09,738] [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 casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	94.8445	958	1225	95	below_threshold
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	94.786	964	1225	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	94.7602	953	1225	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	94.7471	954	1225	95	below_threshold
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	79.9773	408	1225	95	below_threshold
Enterococcus sulfureus	strain=ATCC 49903	GCA_000407025.1	1356	1356	type	True	79.1467	111	1225	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	79.0778	110	1225	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	77.7447	123	1225	95	below_threshold
Enterococcus aquimarinus	strain=DSM 17690	GCA_001885765.1	328396	328396	type	True	77.5143	93	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:09,740] [INFO] DFAST Taxonomy check result was written to GCF_018982785.1_ASM1898278v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:09,740] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:09,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:09,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/checkm_data
[2024-01-24 12:07:09,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:09,776] [INFO] Task started: CheckM
[2024-01-24 12:07:09,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018982785.1_ASM1898278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018982785.1_ASM1898278v1_genomic.fna/checkm_input GCF_018982785.1_ASM1898278v1_genomic.fna/checkm_result
[2024-01-24 12:07:42,453] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:42,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,477] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:42,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:42,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018982785.1_ASM1898278v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:42,479] [INFO] Task started: Blastn
[2024-01-24 12:07:42,479] [INFO] Running command: blastn -query GCF_018982785.1_ASM1898278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg665f6fcd-9460-440b-b5e3-a973d75354a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_018982785.1_ASM1898278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:43,456] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:43,461] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:43,461] [INFO] Target genome list was writen to GCF_018982785.1_ASM1898278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:43,469] [INFO] Task started: fastANI
[2024-01-24 12:07:43,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgc224c3ed-f23b-403c-9f12-e40fa2d49381/GCF_018982785.1_ASM1898278v1_genomic.fna.gz --refList GCF_018982785.1_ASM1898278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018982785.1_ASM1898278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:50,633] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:50,648] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:50,648] [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_002850555.1	s__Enterococcus_D sp002850555	95.6105	1060	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.34	95.31	0.87	0.74	46	conclusive
GCF_001544095.1	s__Enterococcus_D casseliflavus	94.7471	954	1225	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_002140915.1	s__Enterococcus_D sp002140915	80.3529	479	1225	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_001297065.1	s__Enterococcus_D sp001297065	80.0583	482	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCF_001544275.1	s__Enterococcus_D gallinarum	80.0404	410	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.60	97.23	0.85	0.80	74	-
GCF_013394305.1	s__Enterococcus_B pernyi	79.3083	171	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	98.21	97.00	0.90	0.84	22	-
GCF_017426705.1	s__Enterococcus_F sp017426705	78.2623	144	1225	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_017316025.1	s__Enterococcus_C sp017316025	78.0891	114	1225	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_017316305.1	s__Enterococcus_B sp017316305	77.9516	152	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
GCF_000407145.1	s__Enterococcus caccae	77.7526	122	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001885735.1	s__Enterococcus_C canintestini	77.6873	123	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,650] [INFO] GTDB search result was written to GCF_018982785.1_ASM1898278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:50,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:50,653] [INFO] DFAST_QC result json was written to GCF_018982785.1_ASM1898278v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:50,653] [INFO] DFAST_QC completed!
[2024-01-24 12:07:50,654] [INFO] Total running time: 0h0m60s