[2024-01-24 12:31:03,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference
[2024-01-24 12:31:05,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,115] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg5115aa3d-94cf-4d1c-86f4-6ae26193ec42/GCF_004349065.1_ASM434906v1_genomic.fna.gz | prodigal -d GCF_004349065.1_ASM434906v1_genomic.fna/cds.fna -a GCF_004349065.1_ASM434906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:24,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:24,658] [INFO] Task started: HMMsearch
[2024-01-24 12:31:24,658] [INFO] Running command: hmmsearch --tblout GCF_004349065.1_ASM434906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/reference_markers.hmm GCF_004349065.1_ASM434906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:25,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:25,060] [INFO] Found 6/6 markers.
[2024-01-24 12:31:25,120] [INFO] Query marker FASTA was written to GCF_004349065.1_ASM434906v1_genomic.fna/markers.fasta
[2024-01-24 12:31:25,120] [INFO] Task started: Blastn
[2024-01-24 12:31:25,120] [INFO] Running command: blastn -query GCF_004349065.1_ASM434906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/reference_markers.fasta -out GCF_004349065.1_ASM434906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,370] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,374] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:26,375] [INFO] Target genome list was writen to GCF_004349065.1_ASM434906v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:26,382] [INFO] Task started: fastANI
[2024-01-24 12:31:26,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg5115aa3d-94cf-4d1c-86f4-6ae26193ec42/GCF_004349065.1_ASM434906v1_genomic.fna.gz --refList GCF_004349065.1_ASM434906v1_genomic.fna/target_genomes.txt --output GCF_004349065.1_ASM434906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:55,291] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:55,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:55,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:55,309] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:55,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:55,310] [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
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	100.0	2279	2284	95	conclusive
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	85.8342	1353	2284	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	83.9769	1226	2284	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	83.909	1381	2284	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	83.5086	1303	2284	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	83.477	1385	2284	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	83.4477	1269	2284	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	83.4419	1405	2284	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	83.4327	1412	2284	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	83.3865	1381	2284	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	83.3756	1386	2284	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	83.3241	1357	2284	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.5216	355	2284	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	76.485	504	2284	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.3162	719	2284	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	76.2937	661	2284	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	76.1939	505	2284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,312] [INFO] DFAST Taxonomy check result was written to GCF_004349065.1_ASM434906v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:55,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:55,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:55,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/checkm_data
[2024-01-24 12:31:55,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:55,380] [INFO] Task started: CheckM
[2024-01-24 12:31:55,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349065.1_ASM434906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349065.1_ASM434906v1_genomic.fna/checkm_input GCF_004349065.1_ASM434906v1_genomic.fna/checkm_result
[2024-01-24 12:33:02,123] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:02,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:02,149] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:02,150] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:02,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349065.1_ASM434906v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:02,151] [INFO] Task started: Blastn
[2024-01-24 12:33:02,151] [INFO] Running command: blastn -query GCF_004349065.1_ASM434906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4320866-9852-4e3b-b40b-ace9a77cce6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349065.1_ASM434906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:04,043] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:04,048] [INFO] Selected 11 target genomes.
[2024-01-24 12:33:04,049] [INFO] Target genome list was writen to GCF_004349065.1_ASM434906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:04,058] [INFO] Task started: fastANI
[2024-01-24 12:33:04,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg5115aa3d-94cf-4d1c-86f4-6ae26193ec42/GCF_004349065.1_ASM434906v1_genomic.fna.gz --refList GCF_004349065.1_ASM434906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349065.1_ASM434906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:25,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:25,977] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:25,978] [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_004349065.1	s__Jiangella asiatica	100.0	2279	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000515395.1	s__Jiangella gansuensis	85.8173	1355	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003579925.1	s__Jiangella rhizosphaerae	83.9743	1225	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349105.1	s__Jiangella aurantiaca	83.9354	1377	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	83.5116	1302	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	83.494	1384	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900106035.1	s__Jiangella alba	83.4871	1401	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_001270745.1	s__Jiangella muralis	83.4657	1358	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236295.1	s__Jiangella anatolica	83.4286	1271	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204975.1	s__Jiangella mangrovi	83.4147	1377	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003427025.1	s__Jiangella endophytica	83.3484	1353	2284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:25,980] [INFO] GTDB search result was written to GCF_004349065.1_ASM434906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:25,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:25,984] [INFO] DFAST_QC result json was written to GCF_004349065.1_ASM434906v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:25,984] [INFO] DFAST_QC completed!
[2024-01-24 12:33:25,984] [INFO] Total running time: 0h2m22s