[2024-01-25 18:12:20,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:20,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:20,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference
[2024-01-25 18:12:21,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:21,826] [INFO] Task started: Prodigal
[2024-01-25 18:12:21,826] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc21a45d-cf6c-4578-b2e3-134b3cf700f1/GCF_030813515.1_ASM3081351v1_genomic.fna.gz | prodigal -d GCF_030813515.1_ASM3081351v1_genomic.fna/cds.fna -a GCF_030813515.1_ASM3081351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:31,907] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:31,908] [INFO] Task started: HMMsearch
[2024-01-25 18:12:31,908] [INFO] Running command: hmmsearch --tblout GCF_030813515.1_ASM3081351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/reference_markers.hmm GCF_030813515.1_ASM3081351v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:32,140] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:32,142] [INFO] Found 6/6 markers.
[2024-01-25 18:12:32,171] [INFO] Query marker FASTA was written to GCF_030813515.1_ASM3081351v1_genomic.fna/markers.fasta
[2024-01-25 18:12:32,171] [INFO] Task started: Blastn
[2024-01-25 18:12:32,171] [INFO] Running command: blastn -query GCF_030813515.1_ASM3081351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/reference_markers.fasta -out GCF_030813515.1_ASM3081351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:32,995] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:33,000] [INFO] Selected 11 target genomes.
[2024-01-25 18:12:33,001] [INFO] Target genome list was writen to GCF_030813515.1_ASM3081351v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:33,005] [INFO] Task started: fastANI
[2024-01-25 18:12:33,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc21a45d-cf6c-4578-b2e3-134b3cf700f1/GCF_030813515.1_ASM3081351v1_genomic.fna.gz --refList GCF_030813515.1_ASM3081351v1_genomic.fna/target_genomes.txt --output GCF_030813515.1_ASM3081351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:42,335] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:42,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:42,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:42,344] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:12:42,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:12:42,344] [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
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	92.0238	1166	1261	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	91.6594	1152	1261	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	91.6254	1164	1261	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	91.6137	1182	1261	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	79.8257	627	1261	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.3986	268	1261	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.3335	261	1261	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.1418	171	1261	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.8327	185	1261	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.8327	185	1261	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	75.684	101	1261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:42,346] [INFO] DFAST Taxonomy check result was written to GCF_030813515.1_ASM3081351v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:42,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:42,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:42,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/checkm_data
[2024-01-25 18:12:42,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:42,386] [INFO] Task started: CheckM
[2024-01-25 18:12:42,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813515.1_ASM3081351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813515.1_ASM3081351v1_genomic.fna/checkm_input GCF_030813515.1_ASM3081351v1_genomic.fna/checkm_result
[2024-01-25 18:13:15,225] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:15,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:15,245] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:15,245] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:15,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813515.1_ASM3081351v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:15,246] [INFO] Task started: Blastn
[2024-01-25 18:13:15,246] [INFO] Running command: blastn -query GCF_030813515.1_ASM3081351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg760a9aa6-2aeb-42df-a120-073655253ddd/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813515.1_ASM3081351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:16,876] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:16,879] [INFO] Selected 15 target genomes.
[2024-01-25 18:13:16,879] [INFO] Target genome list was writen to GCF_030813515.1_ASM3081351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:16,891] [INFO] Task started: fastANI
[2024-01-25 18:13:16,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc21a45d-cf6c-4578-b2e3-134b3cf700f1/GCF_030813515.1_ASM3081351v1_genomic.fna.gz --refList GCF_030813515.1_ASM3081351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813515.1_ASM3081351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:29,346] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:29,355] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:13:29,356] [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_004023665.1	s__Afifella aestuarii	92.0206	1167	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102695.1	s__Afifella marina	91.6137	1182	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	99.99	99.99	1.00	0.99	5	-
GCF_000688515.1	s__Afifella pfennigii	79.8395	626	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866965.1	s__Propylenella binzhouense	77.5391	299	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110915.1	s__Propylenella sp900110915	77.4948	216	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	77.3882	268	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	77.1201	202	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	76.9954	236	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	76.9793	252	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCA_017307955.1	s__Kaistia sp017307955	76.9585	253	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765365.1	s__VTOM01 sp009765365	76.8402	266	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168115.1	s__Hansschlegelia sp902168115	76.424	189	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	76.1856	84	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002595.1	s__JABDJG01 sp013002595	75.8764	55	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__JABDJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	75.684	101	1261	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:29,357] [INFO] GTDB search result was written to GCF_030813515.1_ASM3081351v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:29,358] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:29,360] [INFO] DFAST_QC result json was written to GCF_030813515.1_ASM3081351v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:29,361] [INFO] DFAST_QC completed!
[2024-01-25 18:13:29,361] [INFO] Total running time: 0h1m9s