[2024-01-24 14:47:08,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference
[2024-01-24 14:47:09,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,977] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg6147e029-e197-45cc-bd3e-f6f2f625974c/GCF_004348545.1_ASM434854v1_genomic.fna.gz | prodigal -d GCF_004348545.1_ASM434854v1_genomic.fna/cds.fna -a GCF_004348545.1_ASM434854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:26,937] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:26,937] [INFO] Task started: HMMsearch
[2024-01-24 14:47:26,937] [INFO] Running command: hmmsearch --tblout GCF_004348545.1_ASM434854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/reference_markers.hmm GCF_004348545.1_ASM434854v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:27,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:27,299] [INFO] Found 6/6 markers.
[2024-01-24 14:47:27,355] [INFO] Query marker FASTA was written to GCF_004348545.1_ASM434854v1_genomic.fna/markers.fasta
[2024-01-24 14:47:27,355] [INFO] Task started: Blastn
[2024-01-24 14:47:27,355] [INFO] Running command: blastn -query GCF_004348545.1_ASM434854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/reference_markers.fasta -out GCF_004348545.1_ASM434854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:28,728] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:28,732] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:28,732] [INFO] Target genome list was writen to GCF_004348545.1_ASM434854v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:28,738] [INFO] Task started: fastANI
[2024-01-24 14:47:28,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg6147e029-e197-45cc-bd3e-f6f2f625974c/GCF_004348545.1_ASM434854v1_genomic.fna.gz --refList GCF_004348545.1_ASM434854v1_genomic.fna/target_genomes.txt --output GCF_004348545.1_ASM434854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:03,223] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:03,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:03,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:03,246] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:03,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:03,247] [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 ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	100.0	2013	2028	95	conclusive
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	91.1785	1725	2028	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	88.2251	1407	2028	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	88.0917	1584	2028	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	87.9587	1608	2028	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	87.6166	1570	2028	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	87.5554	1573	2028	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	87.523	1568	2028	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	87.4762	1506	2028	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	87.364	1489	2028	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	83.5092	1296	2028	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.642	785	2028	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	76.5161	619	2028	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.3052	781	2028	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	76.2522	758	2028	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.1623	675	2028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:03,248] [INFO] DFAST Taxonomy check result was written to GCF_004348545.1_ASM434854v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:03,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:03,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:03,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/checkm_data
[2024-01-24 14:48:03,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:03,310] [INFO] Task started: CheckM
[2024-01-24 14:48:03,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348545.1_ASM434854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348545.1_ASM434854v1_genomic.fna/checkm_input GCF_004348545.1_ASM434854v1_genomic.fna/checkm_result
[2024-01-24 14:49:26,981] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:26,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:27,007] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:27,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:27,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348545.1_ASM434854v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:27,008] [INFO] Task started: Blastn
[2024-01-24 14:49:27,008] [INFO] Running command: blastn -query GCF_004348545.1_ASM434854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7c39e9-68d5-4a73-85b9-6e8390071102/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348545.1_ASM434854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:29,116] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:29,120] [INFO] Selected 11 target genomes.
[2024-01-24 14:49:29,120] [INFO] Target genome list was writen to GCF_004348545.1_ASM434854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:29,130] [INFO] Task started: fastANI
[2024-01-24 14:49:29,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg6147e029-e197-45cc-bd3e-f6f2f625974c/GCF_004348545.1_ASM434854v1_genomic.fna.gz --refList GCF_004348545.1_ASM434854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348545.1_ASM434854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:52,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:52,624] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:52,625] [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_004348545.1	s__Jiangella ureilytica	100.0	2013	2028	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_014204975.1	s__Jiangella mangrovi	91.1881	1724	2028	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	88.1825	1412	2028	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	87.9928	1605	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004349105.1	s__Jiangella aurantiaca	87.9802	1538	2028	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	87.5766	1575	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106035.1	s__Jiangella alba	87.5127	1579	2028	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	87.4748	1506	2028	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	87.3152	1494	2028	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	83.5344	1293	2028	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	83.1388	1225	2028	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 14:49:52,627] [INFO] GTDB search result was written to GCF_004348545.1_ASM434854v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:52,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:52,632] [INFO] DFAST_QC result json was written to GCF_004348545.1_ASM434854v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:52,633] [INFO] DFAST_QC completed!
[2024-01-24 14:49:52,633] [INFO] Total running time: 0h2m44s