[2024-01-24 13:41:41,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,226] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference
[2024-01-24 13:41:42,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,524] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg4291e0db-dbfe-477e-810e-8516bd93f3d9/GCF_001708125.1_ASM170812v1_genomic.fna.gz | prodigal -d GCF_001708125.1_ASM170812v1_genomic.fna/cds.fna -a GCF_001708125.1_ASM170812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:03,662] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:03,663] [INFO] Task started: HMMsearch
[2024-01-24 13:42:03,663] [INFO] Running command: hmmsearch --tblout GCF_001708125.1_ASM170812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/reference_markers.hmm GCF_001708125.1_ASM170812v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:04,018] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:04,020] [INFO] Found 6/6 markers.
[2024-01-24 13:42:04,079] [INFO] Query marker FASTA was written to GCF_001708125.1_ASM170812v1_genomic.fna/markers.fasta
[2024-01-24 13:42:04,080] [INFO] Task started: Blastn
[2024-01-24 13:42:04,080] [INFO] Running command: blastn -query GCF_001708125.1_ASM170812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/reference_markers.fasta -out GCF_001708125.1_ASM170812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:05,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:05,420] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:05,421] [INFO] Target genome list was writen to GCF_001708125.1_ASM170812v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:05,446] [INFO] Task started: fastANI
[2024-01-24 13:42:05,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg4291e0db-dbfe-477e-810e-8516bd93f3d9/GCF_001708125.1_ASM170812v1_genomic.fna.gz --refList GCF_001708125.1_ASM170812v1_genomic.fna/target_genomes.txt --output GCF_001708125.1_ASM170812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:43,009] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:43,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:43,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:43,029] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:42:43,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:43,029] [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 alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	100.0	2541	2542	95	conclusive
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	99.996	2535	2542	95	conclusive
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	93.453	2004	2542	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	89.9411	1907	2542	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	89.3937	1786	2542	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	89.3093	1817	2542	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	88.9899	1554	2542	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	88.7393	1663	2542	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	87.5092	1755	2542	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	87.401	1589	2542	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	83.4626	1398	2542	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	83.4425	1323	2542	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	76.5859	524	2542	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.2824	979	2542	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	76.2067	728	2542	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.0923	787	2542	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.04	819	2542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:43,032] [INFO] DFAST Taxonomy check result was written to GCF_001708125.1_ASM170812v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:43,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:43,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:43,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/checkm_data
[2024-01-24 13:42:43,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:43,107] [INFO] Task started: CheckM
[2024-01-24 13:42:43,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001708125.1_ASM170812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001708125.1_ASM170812v1_genomic.fna/checkm_input GCF_001708125.1_ASM170812v1_genomic.fna/checkm_result
[2024-01-24 13:44:31,108] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:31,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:31,132] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:31,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:31,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001708125.1_ASM170812v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:31,133] [INFO] Task started: Blastn
[2024-01-24 13:44:31,133] [INFO] Running command: blastn -query GCF_001708125.1_ASM170812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7f788d-0f48-464b-a948-4c8a208a011e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001708125.1_ASM170812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:33,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:33,210] [INFO] Selected 10 target genomes.
[2024-01-24 13:44:33,211] [INFO] Target genome list was writen to GCF_001708125.1_ASM170812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:33,256] [INFO] Task started: fastANI
[2024-01-24 13:44:33,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg4291e0db-dbfe-477e-810e-8516bd93f3d9/GCF_001708125.1_ASM170812v1_genomic.fna.gz --refList GCF_001708125.1_ASM170812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001708125.1_ASM170812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:57,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:57,257] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:57,257] [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_900106035.1	s__Jiangella alba	99.996	2535	2542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	conclusive
GCF_001270745.1	s__Jiangella muralis	93.4814	2001	2542	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	89.91	1911	2542	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	89.2538	1825	2542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003579925.1	s__Jiangella rhizosphaerae	88.9886	1554	2542	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	88.704	1668	2542	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	87.5389	1751	2542	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	87.384	1591	2542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	83.4988	1393	2542	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515395.1	s__Jiangella gansuensis	83.435	1325	2542	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 13:44:57,259] [INFO] GTDB search result was written to GCF_001708125.1_ASM170812v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:57,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:57,263] [INFO] DFAST_QC result json was written to GCF_001708125.1_ASM170812v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:57,263] [INFO] DFAST_QC completed!
[2024-01-24 13:44:57,263] [INFO] Total running time: 0h3m16s