[2024-01-24 12:21:44,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference
[2024-01-24 12:21:46,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,038] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48169f6-eb1a-49c3-8e09-55ecf78cffe4/GCF_018283645.1_ASM1828364v1_genomic.fna.gz | prodigal -d GCF_018283645.1_ASM1828364v1_genomic.fna/cds.fna -a GCF_018283645.1_ASM1828364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:04,197] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:04,197] [INFO] Task started: HMMsearch
[2024-01-24 12:22:04,198] [INFO] Running command: hmmsearch --tblout GCF_018283645.1_ASM1828364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/reference_markers.hmm GCF_018283645.1_ASM1828364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:04,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:04,605] [INFO] Found 6/6 markers.
[2024-01-24 12:22:04,669] [INFO] Query marker FASTA was written to GCF_018283645.1_ASM1828364v1_genomic.fna/markers.fasta
[2024-01-24 12:22:04,670] [INFO] Task started: Blastn
[2024-01-24 12:22:04,670] [INFO] Running command: blastn -query GCF_018283645.1_ASM1828364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/reference_markers.fasta -out GCF_018283645.1_ASM1828364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:05,951] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:05,954] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:05,954] [INFO] Target genome list was writen to GCF_018283645.1_ASM1828364v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,962] [INFO] Task started: fastANI
[2024-01-24 12:22:05,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48169f6-eb1a-49c3-8e09-55ecf78cffe4/GCF_018283645.1_ASM1828364v1_genomic.fna.gz --refList GCF_018283645.1_ASM1828364v1_genomic.fna/target_genomes.txt --output GCF_018283645.1_ASM1828364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:42,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:42,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:42,958] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:42,958] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:42,958] [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
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	100.0	2054	2069	95	conclusive
Actinospica robiniae	strain=DSM 44927	GCA_000504285.1	304901	304901	type	True	79.4605	890	2069	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	79.2876	846	2069	95	below_threshold
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	77.9493	701	2069	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	77.88	671	2069	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	77.7297	746	2069	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	77.614	683	2069	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.2728	576	2069	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	77.2188	534	2069	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	77.2004	452	2069	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	77.1947	646	2069	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	77.167	642	2069	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	77.1296	450	2069	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	77.0758	551	2069	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	76.9705	525	2069	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	76.9086	664	2069	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	76.8888	482	2069	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	76.8869	429	2069	95	below_threshold
Streptomyces montanisoli	strain=MMS17-BM035	GCA_017813245.1	2798581	2798581	type	True	76.8162	493	2069	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.6623	367	2069	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	76.3757	492	2069	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	76.1998	507	2069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,960] [INFO] DFAST Taxonomy check result was written to GCF_018283645.1_ASM1828364v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:42,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:42,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:42,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/checkm_data
[2024-01-24 12:22:42,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:43,029] [INFO] Task started: CheckM
[2024-01-24 12:22:43,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018283645.1_ASM1828364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018283645.1_ASM1828364v1_genomic.fna/checkm_input GCF_018283645.1_ASM1828364v1_genomic.fna/checkm_result
[2024-01-24 12:23:39,157] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:39,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:39,184] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:39,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:39,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018283645.1_ASM1828364v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:39,186] [INFO] Task started: Blastn
[2024-01-24 12:23:39,186] [INFO] Running command: blastn -query GCF_018283645.1_ASM1828364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935c8bcc-31e3-45a3-8db6-bba2517bf06a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018283645.1_ASM1828364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:40,956] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:40,961] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:40,962] [INFO] Target genome list was writen to GCF_018283645.1_ASM1828364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:40,974] [INFO] Task started: fastANI
[2024-01-24 12:23:40,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48169f6-eb1a-49c3-8e09-55ecf78cffe4/GCF_018283645.1_ASM1828364v1_genomic.fna.gz --refList GCF_018283645.1_ASM1828364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018283645.1_ASM1828364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:08,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:08,541] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:08,542] [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_018283645.1	s__Actinocrinis puniceicyclus	100.0	2054	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinocrinis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139625.1	s__Actinospica sp018139625	79.5933	845	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504285.1	s__Actinospica robiniae	79.4302	896	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139695.1	s__Actinospica durhamensis	79.2991	843	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361685.1	s__Catenulispora sp013361685	77.8414	650	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356865.1	s__Catenulispora pinisilvae	77.8376	679	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.32	99.32	0.94	0.94	2	-
GCF_018274385.1	s__Catenulispora sp018274385	77.6054	687	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	77.1712	652	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	77.0487	557	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	76.9264	633	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_900105395.1	s__Kitasatospora sp900105395	76.9258	661	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718025.1	s__Kitasatospora purpeofusca	76.9221	660	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.30	95.66	0.88	0.84	3	-
GCF_000719695.1	s__Kitasatospora sp000719695	76.9025	657	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813245.1	s__Streptomyces bomunensis	76.8302	490	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721265.1	s__Streptomyces sp000721265	76.6994	529	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384115.1	s__Sporichthya polymorpha	76.6734	366	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Sporichthyales;f__Sporichthyaceae;g__Sporichthya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082585.1	s__Streptomyces albolongus	76.6558	482	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:08,544] [INFO] GTDB search result was written to GCF_018283645.1_ASM1828364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:08,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:08,551] [INFO] DFAST_QC result json was written to GCF_018283645.1_ASM1828364v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:08,552] [INFO] DFAST_QC completed!
[2024-01-24 12:24:08,552] [INFO] Total running time: 0h2m24s