[2024-01-24 12:05:26,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,620] [INFO] DQC Reference Directory: /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg1174a8ba-4ae0-4516-812a-7936c6640e37/GCF_015356825.1_ASM1535682v1_genomic.fna.gz | prodigal -d GCF_015356825.1_ASM1535682v1_genomic.fna/cds.fna -a GCF_015356825.1_ASM1535682v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:03,597] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:03,597] [INFO] Task started: HMMsearch
[2024-01-24 12:06:03,597] [INFO] Running command: hmmsearch --tblout GCF_015356825.1_ASM1535682v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/reference_markers.hmm GCF_015356825.1_ASM1535682v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:04,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:04,091] [INFO] Found 6/6 markers.
[2024-01-24 12:06:04,189] [INFO] Query marker FASTA was written to GCF_015356825.1_ASM1535682v1_genomic.fna/markers.fasta
[2024-01-24 12:06:04,190] [INFO] Task started: Blastn
[2024-01-24 12:06:04,190] [INFO] Running command: blastn -query GCF_015356825.1_ASM1535682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/reference_markers.fasta -out GCF_015356825.1_ASM1535682v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:05,543] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:05,546] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:05,547] [INFO] Target genome list was writen to GCF_015356825.1_ASM1535682v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:05,556] [INFO] Task started: fastANI
[2024-01-24 12:06:05,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg1174a8ba-4ae0-4516-812a-7936c6640e37/GCF_015356825.1_ASM1535682v1_genomic.fna.gz --refList GCF_015356825.1_ASM1535682v1_genomic.fna/target_genomes.txt --output GCF_015356825.1_ASM1535682v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,669] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,684] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:40,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,684] [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
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	100.0	3880	3903	95	conclusive
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	87.3916	2263	3903	95	below_threshold
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	86.9049	2235	3903	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	86.8954	2183	3903	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	77.6271	755	3903	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	77.3378	914	3903	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	77.2216	944	3903	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	77.1398	724	3903	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	77.0627	728	3903	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.0295	848	3903	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	76.9893	1037	3903	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	76.9115	771	3903	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	76.889	1008	3903	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	76.6644	996	3903	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.3473	677	3903	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	75.9605	475	3903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,686] [INFO] DFAST Taxonomy check result was written to GCF_015356825.1_ASM1535682v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/checkm_data
[2024-01-24 12:06:40,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,803] [INFO] Task started: CheckM
[2024-01-24 12:06:40,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015356825.1_ASM1535682v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015356825.1_ASM1535682v1_genomic.fna/checkm_input GCF_015356825.1_ASM1535682v1_genomic.fna/checkm_result
[2024-01-24 12:08:25,063] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:25,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:25,097] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:25,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:25,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015356825.1_ASM1535682v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:25,098] [INFO] Task started: Blastn
[2024-01-24 12:08:25,098] [INFO] Running command: blastn -query GCF_015356825.1_ASM1535682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9f36e65-2f14-4aa0-9ab5-4da60c8c5a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_015356825.1_ASM1535682v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:27,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:27,233] [INFO] Selected 10 target genomes.
[2024-01-24 12:08:27,234] [INFO] Target genome list was writen to GCF_015356825.1_ASM1535682v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:27,242] [INFO] Task started: fastANI
[2024-01-24 12:08:27,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg1174a8ba-4ae0-4516-812a-7936c6640e37/GCF_015356825.1_ASM1535682v1_genomic.fna.gz --refList GCF_015356825.1_ASM1535682v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015356825.1_ASM1535682v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:50,597] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:50,611] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:50,611] [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_015356825.1	s__Catenulispora rubra	100.0	3880	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024025.1	s__Catenulispora acidiphila	87.3672	2267	3903	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	86.9386	2228	3903	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	86.8958	2182	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	-
GCA_013361685.1	s__Catenulispora sp013361685	83.4802	1572	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362315.1	s__Catenulispora sp013362315	83.2715	1395	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385235.1	s__Amycolatopsis circi	76.0136	661	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	76.0109	700	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_014647915.1	s__Pilimelia terevasa	75.9692	616	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377865.1	s__WHSY01 sp009377865	75.8326	321	3903	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__WHSY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:50,612] [INFO] GTDB search result was written to GCF_015356825.1_ASM1535682v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:50,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:50,618] [INFO] DFAST_QC result json was written to GCF_015356825.1_ASM1535682v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:50,618] [INFO] DFAST_QC completed!
[2024-01-24 12:08:50,619] [INFO] Total running time: 0h3m24s