[2023-06-29 17:18:52,638] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:18:52,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:18:52,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference
[2023-06-29 17:18:54,067] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:18:54,068] [INFO] Task started: Prodigal
[2023-06-29 17:18:54,068] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6210019-d362-4bc1-aa68-586977548d97/GCA_021793295.1_ASM2179329v1_genomic.fna.gz | prodigal -d GCA_021793295.1_ASM2179329v1_genomic.fna/cds.fna -a GCA_021793295.1_ASM2179329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:19:06,883] [INFO] Task succeeded: Prodigal
[2023-06-29 17:19:06,884] [INFO] Task started: HMMsearch
[2023-06-29 17:19:06,884] [INFO] Running command: hmmsearch --tblout GCA_021793295.1_ASM2179329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/reference_markers.hmm GCA_021793295.1_ASM2179329v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:19:07,283] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:19:07,293] [INFO] Found 6/6 markers.
[2023-06-29 17:19:07,336] [INFO] Query marker FASTA was written to GCA_021793295.1_ASM2179329v1_genomic.fna/markers.fasta
[2023-06-29 17:19:07,336] [INFO] Task started: Blastn
[2023-06-29 17:19:07,337] [INFO] Running command: blastn -query GCA_021793295.1_ASM2179329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/reference_markers.fasta -out GCA_021793295.1_ASM2179329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:19:08,669] [INFO] Task succeeded: Blastn
[2023-06-29 17:19:08,676] [INFO] Selected 23 target genomes.
[2023-06-29 17:19:08,676] [INFO] Target genome list was writen to GCA_021793295.1_ASM2179329v1_genomic.fna/target_genomes.txt
[2023-06-29 17:19:08,681] [INFO] Task started: fastANI
[2023-06-29 17:19:08,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6210019-d362-4bc1-aa68-586977548d97/GCA_021793295.1_ASM2179329v1_genomic.fna.gz --refList GCA_021793295.1_ASM2179329v1_genomic.fna/target_genomes.txt --output GCA_021793295.1_ASM2179329v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:19:39,296] [INFO] Task succeeded: fastANI
[2023-06-29 17:19:39,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:19:39,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:19:39,319] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:19:39,319] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:19:39,319] [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
Haloactinopolyspora alba	strain=DSM 45211	GCA_003014555.1	648780	648780	type	True	80.5008	828	1395	95	below_threshold
Haloactinopolyspora alba	strain=YIM 93246	GCA_004138525.1	648780	648780	type	True	80.4771	838	1395	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	80.0289	728	1395	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	79.8836	760	1395	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	79.8322	747	1395	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	79.7741	763	1395	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	79.7418	746	1395	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	79.7404	754	1395	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	79.7227	733	1395	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	79.7029	807	1395	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	79.6572	725	1395	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	79.6423	813	1395	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	79.5633	779	1395	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	79.5618	773	1395	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	79.4955	773	1395	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	76.6482	248	1395	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	76.4824	217	1395	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	76.3116	252	1395	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	76.2445	279	1395	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.2272	359	1395	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	76.1328	310	1395	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	76.0324	245	1395	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	75.9855	294	1395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:19:39,321] [INFO] DFAST Taxonomy check result was written to GCA_021793295.1_ASM2179329v1_genomic.fna/tc_result.tsv
[2023-06-29 17:19:39,322] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:19:39,322] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:19:39,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/checkm_data
[2023-06-29 17:19:39,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:19:39,373] [INFO] Task started: CheckM
[2023-06-29 17:19:39,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021793295.1_ASM2179329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021793295.1_ASM2179329v1_genomic.fna/checkm_input GCA_021793295.1_ASM2179329v1_genomic.fna/checkm_result
[2023-06-29 17:20:23,909] [INFO] Task succeeded: CheckM
[2023-06-29 17:20:23,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:20:23,938] [INFO] ===== Completeness check finished =====
[2023-06-29 17:20:23,938] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:20:23,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021793295.1_ASM2179329v1_genomic.fna/markers.fasta)
[2023-06-29 17:20:23,939] [INFO] Task started: Blastn
[2023-06-29 17:20:23,939] [INFO] Running command: blastn -query GCA_021793295.1_ASM2179329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a990ff1-159c-4125-a4a2-4c25c60c1bc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_021793295.1_ASM2179329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:20:25,670] [INFO] Task succeeded: Blastn
[2023-06-29 17:20:25,675] [INFO] Selected 15 target genomes.
[2023-06-29 17:20:25,676] [INFO] Target genome list was writen to GCA_021793295.1_ASM2179329v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:20:25,683] [INFO] Task started: fastANI
[2023-06-29 17:20:25,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6210019-d362-4bc1-aa68-586977548d97/GCA_021793295.1_ASM2179329v1_genomic.fna.gz --refList GCA_021793295.1_ASM2179329v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021793295.1_ASM2179329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:20:43,753] [INFO] Task succeeded: fastANI
[2023-06-29 17:20:43,767] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 17:20:43,767] [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_003014555.1	s__Haloactinopolyspora alba	80.516	827	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Haloactinopolyspora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003579925.1	s__Jiangella rhizosphaerae	80.0136	730	1395	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	79.9045	757	1395	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	79.8472	745	1395	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	79.7608	765	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270745.1	s__Jiangella muralis	79.7336	755	1395	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	79.7236	732	1395	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	79.7205	749	1395	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	79.685	721	1395	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	79.6402	814	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_900105925.1	s__Jiangella alkaliphila	79.5594	779	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003427025.1	s__Jiangella endophytica	79.5109	771	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424825.1	s__Streptomyces sp000424825	76.4023	248	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704515.1	s__Streptomyces viridosporus	76.3247	261	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_014216315.1	s__Streptomyces finlayi_A	76.1656	219	1395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:20:43,770] [INFO] GTDB search result was written to GCA_021793295.1_ASM2179329v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:20:43,770] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:20:43,775] [INFO] DFAST_QC result json was written to GCA_021793295.1_ASM2179329v1_genomic.fna/dqc_result.json
[2023-06-29 17:20:43,775] [INFO] DFAST_QC completed!
[2023-06-29 17:20:43,775] [INFO] Total running time: 0h1m51s