[2024-01-24 14:46:35,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference
[2024-01-24 14:46:37,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,184] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fed4282-bcd4-4cd7-bd83-07018dcac058/GCF_019890725.1_ASM1989072v1_genomic.fna.gz | prodigal -d GCF_019890725.1_ASM1989072v1_genomic.fna/cds.fna -a GCF_019890725.1_ASM1989072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:59,425] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:59,425] [INFO] Task started: HMMsearch
[2024-01-24 14:46:59,425] [INFO] Running command: hmmsearch --tblout GCF_019890725.1_ASM1989072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/reference_markers.hmm GCF_019890725.1_ASM1989072v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:59,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:59,714] [INFO] Found 6/6 markers.
[2024-01-24 14:46:59,775] [INFO] Query marker FASTA was written to GCF_019890725.1_ASM1989072v1_genomic.fna/markers.fasta
[2024-01-24 14:46:59,775] [INFO] Task started: Blastn
[2024-01-24 14:46:59,775] [INFO] Running command: blastn -query GCF_019890725.1_ASM1989072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/reference_markers.fasta -out GCF_019890725.1_ASM1989072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:01,046] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:01,049] [INFO] Selected 20 target genomes.
[2024-01-24 14:47:01,050] [INFO] Target genome list was writen to GCF_019890725.1_ASM1989072v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:01,057] [INFO] Task started: fastANI
[2024-01-24 14:47:01,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fed4282-bcd4-4cd7-bd83-07018dcac058/GCF_019890725.1_ASM1989072v1_genomic.fna.gz --refList GCF_019890725.1_ASM1989072v1_genomic.fna/target_genomes.txt --output GCF_019890725.1_ASM1989072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:37,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:37,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:37,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:37,740] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:37,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:37,741] [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
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	87.2734	2116	2755	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	83.587	1599	2755	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	83.5489	1329	2755	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	83.5044	1561	2755	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.3624	1557	2755	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	83.3387	1737	2755	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	83.2867	1554	2755	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	83.1389	1688	2755	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	83.1257	1541	2755	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	82.5389	1456	2755	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.8796	1159	2755	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	80.1677	901	2755	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.0227	1137	2755	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	79.9561	907	2755	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	79.9324	1147	2755	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	79.9068	1187	2755	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.9004	1182	2755	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	79.8386	1150	2755	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	79.7004	1129	2755	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	79.4338	1156	2755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:37,742] [INFO] DFAST Taxonomy check result was written to GCF_019890725.1_ASM1989072v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:37,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:37,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:37,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/checkm_data
[2024-01-24 14:47:37,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:37,816] [INFO] Task started: CheckM
[2024-01-24 14:47:37,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019890725.1_ASM1989072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019890725.1_ASM1989072v1_genomic.fna/checkm_input GCF_019890725.1_ASM1989072v1_genomic.fna/checkm_result
[2024-01-24 14:49:37,172] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:37,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:37,199] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:37,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:37,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019890725.1_ASM1989072v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:37,200] [INFO] Task started: Blastn
[2024-01-24 14:49:37,200] [INFO] Running command: blastn -query GCF_019890725.1_ASM1989072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff272c92-b833-45c9-baeb-f0c55b93958c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019890725.1_ASM1989072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:39,439] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:39,443] [INFO] Selected 18 target genomes.
[2024-01-24 14:49:39,443] [INFO] Target genome list was writen to GCF_019890725.1_ASM1989072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:39,458] [INFO] Task started: fastANI
[2024-01-24 14:49:39,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fed4282-bcd4-4cd7-bd83-07018dcac058/GCF_019890725.1_ASM1989072v1_genomic.fna.gz --refList GCF_019890725.1_ASM1989072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019890725.1_ASM1989072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:17,329] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:17,344] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:50:17,345] [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
GCA_009783685.1	s__Streptomyces sp009783685	87.8586	1181	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110255.1	s__Streptomyces rubidus	87.2971	2112	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112845.1	s__Streptomyces alni	83.583	1601	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	83.4853	1564	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900103985.1	s__Streptomyces guanduensis	83.3468	1562	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918855.1	s__Streptomyces acididurans	83.3321	1739	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	83.304	1550	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	83.2493	1514	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	83.1346	1539	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107965.1	s__Streptomyces yanglinensis	83.0803	1701	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756395.1	s__Streptomyces sp016756395	83.0168	1533	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	82.8655	1489	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745345.1	s__Streptomyces yeochonensis	82.4905	1465	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	80.0168	1191	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000715845.1	s__Streptomyces monomycini	79.9465	1143	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031615.1	s__Streptomyces pactum	79.9318	1183	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	79.8602	1101	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_014656075.1	s__Streptomyces hydrogenans	79.8523	1151	2755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:17,346] [INFO] GTDB search result was written to GCF_019890725.1_ASM1989072v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:17,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:17,351] [INFO] DFAST_QC result json was written to GCF_019890725.1_ASM1989072v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:17,351] [INFO] DFAST_QC completed!
[2024-01-24 14:50:17,351] [INFO] Total running time: 0h3m42s