[2024-01-24 14:06:45,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:45,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:45,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference
[2024-01-24 14:06:46,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,798] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,798] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6f45beb-cc5c-49f7-83f6-9e1d584c3037/GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna.gz | prodigal -d GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/cds.fna -a GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:02,858] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:02,859] [INFO] Task started: HMMsearch
[2024-01-24 14:07:02,859] [INFO] Running command: hmmsearch --tblout GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/reference_markers.hmm GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:03,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:03,171] [INFO] Found 6/6 markers.
[2024-01-24 14:07:03,230] [INFO] Query marker FASTA was written to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/markers.fasta
[2024-01-24 14:07:03,231] [INFO] Task started: Blastn
[2024-01-24 14:07:03,231] [INFO] Running command: blastn -query GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/reference_markers.fasta -out GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,487] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,494] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:04,494] [INFO] Target genome list was writen to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/target_genomes.txt
[2024-01-24 14:07:04,511] [INFO] Task started: fastANI
[2024-01-24 14:07:04,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f45beb-cc5c-49f7-83f6-9e1d584c3037/GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna.gz --refList GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/target_genomes.txt --output GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:35,314] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:35,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:35,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:35,337] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:35,337] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:07:35,338] [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
Streptomyces xiaopingdaonensis	strain=DUT 180	GCA_000262345.1	1565415	1565415	type	True	100.0	1952	1966	95	inconclusive
Streptomyces sulphureus	strain=DSM 40104	GCA_000381025.1	47758	47758	type	True	95.1625	1794	1966	95	inconclusive
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	80.7764	1039	1966	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	80.7373	965	1966	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	80.7022	1050	1966	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	80.665	1084	1966	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	80.524	960	1966	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	80.4758	1089	1966	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	80.4286	891	1966	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.386	1005	1966	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.3341	942	1966	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	79.9197	810	1966	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	79.8835	857	1966	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	79.8106	809	1966	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	79.518	907	1966	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	79.4732	891	1966	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	79.4509	908	1966	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	79.44	909	1966	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.3789	900	1966	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	79.3382	899	1966	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	79.3122	920	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:35,340] [INFO] DFAST Taxonomy check result was written to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/tc_result.tsv
[2024-01-24 14:07:35,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:35,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:35,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/checkm_data
[2024-01-24 14:07:35,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:35,407] [INFO] Task started: CheckM
[2024-01-24 14:07:35,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/checkm_input GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/checkm_result
[2024-01-24 14:08:48,659] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:48,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:48,683] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:48,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:48,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/markers.fasta)
[2024-01-24 14:08:48,684] [INFO] Task started: Blastn
[2024-01-24 14:08:48,684] [INFO] Running command: blastn -query GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ed17e7-84de-4129-93cb-d1f9d1bcd491/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:50,816] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:50,821] [INFO] Selected 18 target genomes.
[2024-01-24 14:08:50,822] [INFO] Target genome list was writen to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:50,835] [INFO] Task started: fastANI
[2024-01-24 14:08:50,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f45beb-cc5c-49f7-83f6-9e1d584c3037/GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna.gz --refList GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:17,532] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:17,551] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:17,552] [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_000262345.1	s__Streptomyces xiaopingdaonensis	100.0	1952	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1625	N/A	N/A	N/A	N/A	1	conclusive
GCF_000381025.1	s__Streptomyces sulphureus	95.1625	1794	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1625	N/A	N/A	N/A	N/A	1	conclusive
GCF_012726235.1	s__Streptomyces sp012726235	80.8968	1028	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539165.1	s__Streptomyces cacaoi	80.6712	1084	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
GCF_003323735.1	s__Streptomyces reniochalinae	80.6592	1057	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676385.1	s__Streptomyces sp017676385	80.5484	956	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	80.5274	1056	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	80.5148	1035	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323715.1	s__Streptomyces diacarni	80.4966	1086	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	80.4157	1000	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_017676365.1	s__Streptomyces oryzae	80.3344	942	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418285.1	s__Streptomyces sp001418285	80.1825	877	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.71	95.43	0.94	0.89	3	-
GCF_001418495.1	s__Streptomyces pathocidini	80.1622	665	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	79.9421	807	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_900110735.1	s__Streptomyces radiopugnans	79.9115	852	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	79.7809	813	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCA_000720555.1	s__Streptomyces sclerotialus	79.657	906	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741875.1	s__Streptomyces coffeae	79.0743	833	1966	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 14:09:17,554] [INFO] GTDB search result was written to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:17,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:17,561] [INFO] DFAST_QC result json was written to GCF_000262345.1_Streptomyces_sulphureus_L180_version_1.0_genomic.fna/dqc_result.json
[2024-01-24 14:09:17,562] [INFO] DFAST_QC completed!
[2024-01-24 14:09:17,562] [INFO] Total running time: 0h2m32s