[2024-01-24 14:14:31,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference
[2024-01-24 14:14:33,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,027] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc9487c-1343-4084-afbb-3439da2bdc05/GCF_012034935.1_ASM1203493v1_genomic.fna.gz | prodigal -d GCF_012034935.1_ASM1203493v1_genomic.fna/cds.fna -a GCF_012034935.1_ASM1203493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:50,189] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:50,190] [INFO] Task started: HMMsearch
[2024-01-24 14:14:50,190] [INFO] Running command: hmmsearch --tblout GCF_012034935.1_ASM1203493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/reference_markers.hmm GCF_012034935.1_ASM1203493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:50,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:50,546] [INFO] Found 6/6 markers.
[2024-01-24 14:14:50,597] [INFO] Query marker FASTA was written to GCF_012034935.1_ASM1203493v1_genomic.fna/markers.fasta
[2024-01-24 14:14:50,598] [INFO] Task started: Blastn
[2024-01-24 14:14:50,598] [INFO] Running command: blastn -query GCF_012034935.1_ASM1203493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/reference_markers.fasta -out GCF_012034935.1_ASM1203493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:51,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:51,908] [INFO] Selected 27 target genomes.
[2024-01-24 14:14:51,909] [INFO] Target genome list was writen to GCF_012034935.1_ASM1203493v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:51,925] [INFO] Task started: fastANI
[2024-01-24 14:14:51,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc9487c-1343-4084-afbb-3439da2bdc05/GCF_012034935.1_ASM1203493v1_genomic.fna.gz --refList GCF_012034935.1_ASM1203493v1_genomic.fna/target_genomes.txt --output GCF_012034935.1_ASM1203493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:39,546] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:39,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:39,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:39,574] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:39,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:39,574] [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 xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	84.8564	1517	2134	95	below_threshold
Streptomyces lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	82.4081	1219	2134	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.9802	917	2134	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	80.665	1048	2134	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	80.6283	1027	2134	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	80.6107	1050	2134	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	80.5614	1044	2134	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	80.5512	930	2134	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	80.535	996	2134	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	80.5171	1075	2134	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.4178	1113	2134	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	80.4135	1093	2134	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.4043	1091	2134	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	80.3903	1074	2134	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	80.3794	1130	2134	95	below_threshold
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	80.3609	1081	2134	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	80.345	1047	2134	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	80.3363	1164	2134	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	80.299	1181	2134	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	80.2951	972	2134	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	80.2704	1087	2134	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.2663	1048	2134	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.2522	1234	2134	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	80.1265	1087	2134	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.8861	1141	2134	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	79.7719	1049	2134	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	79.6679	1049	2134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:39,579] [INFO] DFAST Taxonomy check result was written to GCF_012034935.1_ASM1203493v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:39,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:39,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:39,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/checkm_data
[2024-01-24 14:15:39,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:39,656] [INFO] Task started: CheckM
[2024-01-24 14:15:39,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034935.1_ASM1203493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034935.1_ASM1203493v1_genomic.fna/checkm_input GCF_012034935.1_ASM1203493v1_genomic.fna/checkm_result
[2024-01-24 14:17:10,892] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:10,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:10,919] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:10,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:10,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034935.1_ASM1203493v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:10,920] [INFO] Task started: Blastn
[2024-01-24 14:17:10,920] [INFO] Running command: blastn -query GCF_012034935.1_ASM1203493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ca14b57-9b7e-4a55-a877-92ee71454721/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034935.1_ASM1203493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:12,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:12,996] [INFO] Selected 12 target genomes.
[2024-01-24 14:17:12,996] [INFO] Target genome list was writen to GCF_012034935.1_ASM1203493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:13,006] [INFO] Task started: fastANI
[2024-01-24 14:17:13,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc9487c-1343-4084-afbb-3439da2bdc05/GCF_012034935.1_ASM1203493v1_genomic.fna.gz --refList GCF_012034935.1_ASM1203493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034935.1_ASM1203493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:33,469] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:33,480] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:33,480] [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_012034935.1	s__Streptomyces sp012034935	100.0	2132	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000220705.2	s__Streptomyces xinghaiensis	84.9088	1509	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.52	96.44	0.86	0.81	7	-
GCF_000719865.1	s__Streptomyces albus_E	84.8502	1444	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070345.1	s__Streptomyces sp018070345	84.6105	1425	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002573955.1	s__Streptomyces sp002573955	82.4914	1194	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.87	0.87	2	-
GCF_001418495.1	s__Streptomyces pathocidini	81.5787	813	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715685.1	s__Streptomyces lilacinus	80.6709	1015	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158915.1	s__Streptomyces himastatinicus	80.3892	1195	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
GCF_014295035.1	s__Streptomyces buecherae	80.2386	1093	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
GCF_000719335.1	s__Streptomyces sp000719335	79.8937	1043	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424845.1	s__Streptomyces sp000424845	79.8631	923	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704935.1	s__Streptomyces vinaceus	79.7119	1033	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:33,482] [INFO] GTDB search result was written to GCF_012034935.1_ASM1203493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:33,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:33,487] [INFO] DFAST_QC result json was written to GCF_012034935.1_ASM1203493v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:33,487] [INFO] DFAST_QC completed!
[2024-01-24 14:17:33,487] [INFO] Total running time: 0h3m2s