[2024-01-24 12:06:33,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,743] [INFO] DQC Reference Directory: /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference
[2024-01-24 12:06:35,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,071] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,071] [INFO] Running command: gunzip -c /var/lib/cwl/stgc43e9e52-1ba1-4c0d-968d-1a58813bf12f/GCF_900604485.1_PRJEB28790_genomic.fna.gz | prodigal -d GCF_900604485.1_PRJEB28790_genomic.fna/cds.fna -a GCF_900604485.1_PRJEB28790_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:41,796] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:41,797] [INFO] Task started: HMMsearch
[2024-01-24 12:06:41,797] [INFO] Running command: hmmsearch --tblout GCF_900604485.1_PRJEB28790_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/reference_markers.hmm GCF_900604485.1_PRJEB28790_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:42,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:42,059] [INFO] Found 6/6 markers.
[2024-01-24 12:06:42,088] [INFO] Query marker FASTA was written to GCF_900604485.1_PRJEB28790_genomic.fna/markers.fasta
[2024-01-24 12:06:42,088] [INFO] Task started: Blastn
[2024-01-24 12:06:42,088] [INFO] Running command: blastn -query GCF_900604485.1_PRJEB28790_genomic.fna/markers.fasta -db /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/reference_markers.fasta -out GCF_900604485.1_PRJEB28790_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:42,684] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:42,688] [INFO] Selected 22 target genomes.
[2024-01-24 12:06:42,688] [INFO] Target genome list was writen to GCF_900604485.1_PRJEB28790_genomic.fna/target_genomes.txt
[2024-01-24 12:06:42,696] [INFO] Task started: fastANI
[2024-01-24 12:06:42,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43e9e52-1ba1-4c0d-968d-1a58813bf12f/GCF_900604485.1_PRJEB28790_genomic.fna.gz --refList GCF_900604485.1_PRJEB28790_genomic.fna/target_genomes.txt --output GCF_900604485.1_PRJEB28790_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:52,639] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:52,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:52,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:52,656] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:52,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:52,657] [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	100.0	898	898	95	conclusive
Enterococcus dispar	strain=ATCC 51266	GCA_000407585.1	44009	44009	type	True	80.312	144	898	95	below_threshold
Enterococcus durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	79.9447	164	898	95	below_threshold
Enterococcus dispar	strain=ATCC 51266	GCA_000406945.1	44009	44009	type	True	79.8645	135	898	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	79.4666	157	898	95	below_threshold
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	79.3622	177	898	95	below_threshold
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	79.2207	183	898	95	below_threshold
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	79.1715	131	898	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	78.756	158	898	95	below_threshold
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	78.6918	182	898	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	78.6685	176	898	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	78.6034	171	898	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	78.5927	102	898	95	below_threshold
Enterococcus mundtii	strain=NBRC 100490	GCA_007990125.1	53346	53346	type	True	78.2021	154	898	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_001886035.1	53346	53346	type	True	78.1252	154	898	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	78.0999	123	898	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	77.7384	93	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:52,658] [INFO] DFAST Taxonomy check result was written to GCF_900604485.1_PRJEB28790_genomic.fna/tc_result.tsv
[2024-01-24 12:06:52,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:52,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:52,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/checkm_data
[2024-01-24 12:06:52,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:52,693] [INFO] Task started: CheckM
[2024-01-24 12:06:52,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604485.1_PRJEB28790_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604485.1_PRJEB28790_genomic.fna/checkm_input GCF_900604485.1_PRJEB28790_genomic.fna/checkm_result
[2024-01-24 12:07:18,952] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:18,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:18,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:18,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604485.1_PRJEB28790_genomic.fna/markers.fasta)
[2024-01-24 12:07:18,974] [INFO] Task started: Blastn
[2024-01-24 12:07:18,974] [INFO] Running command: blastn -query GCF_900604485.1_PRJEB28790_genomic.fna/markers.fasta -db /var/lib/cwl/stge7adbb6c-b934-44db-b207-936a38c897fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604485.1_PRJEB28790_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,745] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,749] [INFO] Selected 21 target genomes.
[2024-01-24 12:07:19,749] [INFO] Target genome list was writen to GCF_900604485.1_PRJEB28790_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:19,764] [INFO] Task started: fastANI
[2024-01-24 12:07:19,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43e9e52-1ba1-4c0d-968d-1a58813bf12f/GCF_900604485.1_PRJEB28790_genomic.fna.gz --refList GCF_900604485.1_PRJEB28790_genomic.fna/target_genomes_gtdb.txt --output GCF_900604485.1_PRJEB28790_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:30,685] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:30,706] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:30,707] [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_900604485.1	s__Enterococcus_C mediterraneensis	100.0	898	898	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_000406945.1	s__Enterococcus_C dispar	79.8245	135	898	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_001544215.1	s__Enterococcus_B durans	79.3939	155	898	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_003957375.1	s__Enterococcus_B mundtii_C	79.3849	152	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.247	99.65	99.65	0.94	0.94	2	-
GCF_005405265.1	s__Enterococcus_C songbeiensis	79.3661	349	898	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_011038845.1	s__Enterococcus_B sp011038845	79.0224	163	898	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_002813755.1	s__Enterococcus_B mundtii	78.8699	159	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCF_002141365.1	s__Enterococcus sp002141365	78.8689	100	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394305.1	s__Enterococcus_B pernyi	78.8402	154	898	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_002850555.1	s__Enterococcus_D sp002850555	78.8236	194	898	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_001544275.1	s__Enterococcus_D gallinarum	78.7737	185	898	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_001544095.1	s__Enterococcus_D casseliflavus	78.6685	176	898	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_000415185.1	s__Enterococcus_B faecalis_A	78.6228	157	898	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_005405205.1	s__Enterococcus_A pingfangensis	78.5308	114	898	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_001297065.1	s__Enterococcus_D sp001297065	78.1457	173	898	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_002197645.1	s__Enterococcus wangshanyuanii	78.107	131	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001730295.1	s__Enterococcus plantarum	78.0256	92	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_009933135.1	s__Enterococcus_C sp009933135	77.9586	145	898	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_018917525.1	s__Enterococcus_A raffinosus_A	77.6251	122	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:30,710] [INFO] GTDB search result was written to GCF_900604485.1_PRJEB28790_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:30,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:30,718] [INFO] DFAST_QC result json was written to GCF_900604485.1_PRJEB28790_genomic.fna/dqc_result.json
[2024-01-24 12:07:30,718] [INFO] DFAST_QC completed!
[2024-01-24 12:07:30,718] [INFO] Total running time: 0h0m57s