[2024-01-24 12:13:54,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:54,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:54,732] [INFO] DQC Reference Directory: /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference
[2024-01-24 12:13:57,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,517] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbc1611e-56da-4c17-9193-d3bfd09b54d1/GCF_003236295.1_ASM323629v1_genomic.fna.gz | prodigal -d GCF_003236295.1_ASM323629v1_genomic.fna/cds.fna -a GCF_003236295.1_ASM323629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,724] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,724] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,725] [INFO] Running command: hmmsearch --tblout GCF_003236295.1_ASM323629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/reference_markers.hmm GCF_003236295.1_ASM323629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:16,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:16,144] [INFO] Found 6/6 markers.
[2024-01-24 12:14:16,219] [INFO] Query marker FASTA was written to GCF_003236295.1_ASM323629v1_genomic.fna/markers.fasta
[2024-01-24 12:14:16,220] [INFO] Task started: Blastn
[2024-01-24 12:14:16,220] [INFO] Running command: blastn -query GCF_003236295.1_ASM323629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/reference_markers.fasta -out GCF_003236295.1_ASM323629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:17,665] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:17,668] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:17,668] [INFO] Target genome list was writen to GCF_003236295.1_ASM323629v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:17,675] [INFO] Task started: fastANI
[2024-01-24 12:14:17,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc1611e-56da-4c17-9193-d3bfd09b54d1/GCF_003236295.1_ASM323629v1_genomic.fna.gz --refList GCF_003236295.1_ASM323629v1_genomic.fna/target_genomes.txt --output GCF_003236295.1_ASM323629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:50,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:50,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:50,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:50,186] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:50,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:50,186] [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 anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	100.0	2212	2224	95	conclusive
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	88.7453	1683	2224	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	88.7285	1702	2224	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	88.696	1693	2224	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	88.6417	1675	2224	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	88.6326	1562	2224	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	88.4969	1447	2224	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	88.297	1511	2224	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	87.3109	1501	2224	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	87.2388	1627	2224	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.9754	604	2224	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.5864	873	2224	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.3481	897	2224	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.3403	813	2224	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.2907	749	2224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:50,188] [INFO] DFAST Taxonomy check result was written to GCF_003236295.1_ASM323629v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:50,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:50,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:50,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/checkm_data
[2024-01-24 12:14:50,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:50,256] [INFO] Task started: CheckM
[2024-01-24 12:14:50,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003236295.1_ASM323629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003236295.1_ASM323629v1_genomic.fna/checkm_input GCF_003236295.1_ASM323629v1_genomic.fna/checkm_result
[2024-01-24 12:16:16,348] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:16,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,375] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:16,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:16,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003236295.1_ASM323629v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:16,376] [INFO] Task started: Blastn
[2024-01-24 12:16:16,377] [INFO] Running command: blastn -query GCF_003236295.1_ASM323629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb724c622-463c-4535-933f-7002375357c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003236295.1_ASM323629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:18,589] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:18,593] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:18,593] [INFO] Target genome list was writen to GCF_003236295.1_ASM323629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:18,601] [INFO] Task started: fastANI
[2024-01-24 12:16:18,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc1611e-56da-4c17-9193-d3bfd09b54d1/GCF_003236295.1_ASM323629v1_genomic.fna.gz --refList GCF_003236295.1_ASM323629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003236295.1_ASM323629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:40,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:40,474] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:40,475] [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_003236295.1	s__Jiangella anatolica	100.0	2212	2224	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_900105925.1	s__Jiangella alkaliphila	88.7257	1703	2224	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	88.638	1674	2224	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	88.6254	1563	2224	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	88.4888	1448	2224	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	88.2978	1511	2224	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	88.0757	1651	2224	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	87.3214	1500	2224	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	87.2686	1623	2224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014555.1	s__Haloactinopolyspora alba	80.4126	939	2224	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Haloactinopolyspora	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,480] [INFO] GTDB search result was written to GCF_003236295.1_ASM323629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:40,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:40,487] [INFO] DFAST_QC result json was written to GCF_003236295.1_ASM323629v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:40,487] [INFO] DFAST_QC completed!
[2024-01-24 12:16:40,487] [INFO] Total running time: 0h2m46s