[2023-06-30 18:10:52,827] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:10:52,830] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:10:52,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference
[2023-06-30 18:10:55,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:10:55,685] [INFO] Task started: Prodigal
[2023-06-30 18:10:55,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg183edeb1-b8bc-4d6a-88b7-a72e03212716/GCA_025964585.1_ASM2596458v1_genomic.fna.gz | prodigal -d GCA_025964585.1_ASM2596458v1_genomic.fna/cds.fna -a GCA_025964585.1_ASM2596458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:11:11,912] [INFO] Task succeeded: Prodigal
[2023-06-30 18:11:11,913] [INFO] Task started: HMMsearch
[2023-06-30 18:11:11,913] [INFO] Running command: hmmsearch --tblout GCA_025964585.1_ASM2596458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/reference_markers.hmm GCA_025964585.1_ASM2596458v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:11:12,227] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:11:12,229] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg183edeb1-b8bc-4d6a-88b7-a72e03212716/GCA_025964585.1_ASM2596458v1_genomic.fna.gz]
[2023-06-30 18:11:12,292] [INFO] Query marker FASTA was written to GCA_025964585.1_ASM2596458v1_genomic.fna/markers.fasta
[2023-06-30 18:11:12,292] [INFO] Task started: Blastn
[2023-06-30 18:11:12,293] [INFO] Running command: blastn -query GCA_025964585.1_ASM2596458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/reference_markers.fasta -out GCA_025964585.1_ASM2596458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:11:13,162] [INFO] Task succeeded: Blastn
[2023-06-30 18:11:13,167] [INFO] Selected 22 target genomes.
[2023-06-30 18:11:13,168] [INFO] Target genome list was writen to GCA_025964585.1_ASM2596458v1_genomic.fna/target_genomes.txt
[2023-06-30 18:11:13,173] [INFO] Task started: fastANI
[2023-06-30 18:11:13,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg183edeb1-b8bc-4d6a-88b7-a72e03212716/GCA_025964585.1_ASM2596458v1_genomic.fna.gz --refList GCA_025964585.1_ASM2596458v1_genomic.fna/target_genomes.txt --output GCA_025964585.1_ASM2596458v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:11:41,340] [INFO] Task succeeded: fastANI
[2023-06-30 18:11:41,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:11:41,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:11:41,361] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:11:41,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:11:41,361] [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
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	82.7344	1180	1957	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	76.7046	416	1957	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	76.539	462	1957	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	76.4362	507	1957	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	76.4359	436	1957	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	76.4322	549	1957	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	76.4288	495	1957	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	76.4263	441	1957	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	76.4142	508	1957	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	76.3902	440	1957	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	76.3496	443	1957	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	76.344	394	1957	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	76.3311	424	1957	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	76.3288	474	1957	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	75.9669	419	1957	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	75.8895	364	1957	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	75.8643	475	1957	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	75.8546	374	1957	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	75.8369	429	1957	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	75.7672	219	1957	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	75.6258	359	1957	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	75.6011	269	1957	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:11:41,366] [INFO] DFAST Taxonomy check result was written to GCA_025964585.1_ASM2596458v1_genomic.fna/tc_result.tsv
[2023-06-30 18:11:41,368] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:11:41,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:11:41,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/checkm_data
[2023-06-30 18:11:41,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:11:41,440] [INFO] Task started: CheckM
[2023-06-30 18:11:41,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025964585.1_ASM2596458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025964585.1_ASM2596458v1_genomic.fna/checkm_input GCA_025964585.1_ASM2596458v1_genomic.fna/checkm_result
[2023-06-30 18:12:29,566] [INFO] Task succeeded: CheckM
[2023-06-30 18:12:29,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 10.94%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 18:12:29,596] [INFO] ===== Completeness check finished =====
[2023-06-30 18:12:29,596] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:12:29,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025964585.1_ASM2596458v1_genomic.fna/markers.fasta)
[2023-06-30 18:12:29,597] [INFO] Task started: Blastn
[2023-06-30 18:12:29,597] [INFO] Running command: blastn -query GCA_025964585.1_ASM2596458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b7a596-5956-4834-8744-04b5bf563a72/dqc_reference/reference_markers_gtdb.fasta -out GCA_025964585.1_ASM2596458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:12:30,935] [INFO] Task succeeded: Blastn
[2023-06-30 18:12:30,940] [INFO] Selected 15 target genomes.
[2023-06-30 18:12:30,941] [INFO] Target genome list was writen to GCA_025964585.1_ASM2596458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:12:30,973] [INFO] Task started: fastANI
[2023-06-30 18:12:30,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg183edeb1-b8bc-4d6a-88b7-a72e03212716/GCA_025964585.1_ASM2596458v1_genomic.fna.gz --refList GCA_025964585.1_ASM2596458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025964585.1_ASM2596458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:12:49,404] [INFO] Task succeeded: fastANI
[2023-06-30 18:12:49,419] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 18:12:49,419] [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_007827045.1	s__Trebonia kvetii	82.7245	1181	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017354375.1	s__Trebonia sp017354375	79.1156	564	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239975.1	s__JAFAZE01 sp019239975	78.5492	657	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFAZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009784565.1	s__Trebonia sp009784565	78.3055	589	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240215.1	s__Bog-532 sp019240215	77.7561	411	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245115.1	s__JAFARZ01 sp019245115	77.542	581	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFARZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168255.1	s__PALSA-505 sp003168255	77.0256	421	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__PALSA-505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541285.1	s__UBA9676 sp003541285	76.8153	323	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__UBA9676	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	76.4531	567	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	76.4337	506	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	76.3774	443	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	76.3694	420	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570405.1	s__Microtetraspora niveoalba	76.3374	446	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	76.3301	397	1957	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785715.1	s__WQVT01 sp009785715	75.3412	75	1957	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__WQVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:12:49,421] [INFO] GTDB search result was written to GCA_025964585.1_ASM2596458v1_genomic.fna/result_gtdb.tsv
[2023-06-30 18:12:49,422] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:12:49,426] [INFO] DFAST_QC result json was written to GCA_025964585.1_ASM2596458v1_genomic.fna/dqc_result.json
[2023-06-30 18:12:49,427] [INFO] DFAST_QC completed!
[2023-06-30 18:12:49,427] [INFO] Total running time: 0h1m57s