[2024-01-24 10:48:09,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg130e1b94-3e2d-40fb-a3ec-26b0110c67af/GCF_014650935.1_ASM1465093v1_genomic.fna.gz | prodigal -d GCF_014650935.1_ASM1465093v1_genomic.fna/cds.fna -a GCF_014650935.1_ASM1465093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:44,662] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:44,662] [INFO] Task started: HMMsearch
[2024-01-24 10:48:44,662] [INFO] Running command: hmmsearch --tblout GCF_014650935.1_ASM1465093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/reference_markers.hmm GCF_014650935.1_ASM1465093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:45,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:45,015] [INFO] Found 6/6 markers.
[2024-01-24 10:48:45,079] [INFO] Query marker FASTA was written to GCF_014650935.1_ASM1465093v1_genomic.fna/markers.fasta
[2024-01-24 10:48:45,079] [INFO] Task started: Blastn
[2024-01-24 10:48:45,080] [INFO] Running command: blastn -query GCF_014650935.1_ASM1465093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/reference_markers.fasta -out GCF_014650935.1_ASM1465093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,512] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,518] [INFO] Selected 25 target genomes.
[2024-01-24 10:48:46,519] [INFO] Target genome list was writen to GCF_014650935.1_ASM1465093v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:46,565] [INFO] Task started: fastANI
[2024-01-24 10:48:46,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg130e1b94-3e2d-40fb-a3ec-26b0110c67af/GCF_014650935.1_ASM1465093v1_genomic.fna.gz --refList GCF_014650935.1_ASM1465093v1_genomic.fna/target_genomes.txt --output GCF_014650935.1_ASM1465093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:31,798] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:31,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:31,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:31,820] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:49:31,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:31,820] [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 subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	100.0	2544	2549	95	conclusive
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	99.9974	2470	2549	95	conclusive
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	87.8407	1760	2549	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	87.7775	1775	2549	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	87.6453	1767	2549	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	87.6235	1733	2549	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	87.5876	1766	2549	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	87.5465	1782	2549	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	87.5239	1768	2549	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	87.3355	1744	2549	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.8208	1005	2549	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.693	1054	2549	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	81.6243	1076	2549	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	81.2488	1359	2549	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	81.0604	1348	2549	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.0439	1302	2549	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	81.0377	1330	2549	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	80.9045	1081	2549	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.7427	1160	2549	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	80.6905	1150	2549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:31,822] [INFO] DFAST Taxonomy check result was written to GCF_014650935.1_ASM1465093v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:31,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:31,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:31,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/checkm_data
[2024-01-24 10:49:31,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:31,901] [INFO] Task started: CheckM
[2024-01-24 10:49:31,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650935.1_ASM1465093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650935.1_ASM1465093v1_genomic.fna/checkm_input GCF_014650935.1_ASM1465093v1_genomic.fna/checkm_result
[2024-01-24 10:51:06,165] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:06,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:06,194] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:06,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:06,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650935.1_ASM1465093v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:06,195] [INFO] Task started: Blastn
[2024-01-24 10:51:06,196] [INFO] Running command: blastn -query GCF_014650935.1_ASM1465093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg962781df-6eb1-4652-919d-7109f5696585/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650935.1_ASM1465093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:08,628] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:08,633] [INFO] Selected 28 target genomes.
[2024-01-24 10:51:08,633] [INFO] Target genome list was writen to GCF_014650935.1_ASM1465093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:08,686] [INFO] Task started: fastANI
[2024-01-24 10:51:08,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg130e1b94-3e2d-40fb-a3ec-26b0110c67af/GCF_014650935.1_ASM1465093v1_genomic.fna.gz --refList GCF_014650935.1_ASM1465093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650935.1_ASM1465093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:55,662] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:55,684] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:55,684] [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_008704535.1	s__Streptomyces subrutilus	99.9974	2470	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCF_018614075.1	s__Streptomyces sp018614075	88.1324	1591	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614155.1	s__Streptomyces sp018614155	88.0345	1630	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720115.1	s__Streptomyces sp000720115	87.8879	1714	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725805.1	s__Streptomyces xanthophaeus	87.8596	1759	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
GCF_001746425.1	s__Streptomyces subrutilus_A	87.857	1683	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080455.1	s__Streptomyces sp002080455	87.8428	1758	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_001905445.1	s__Streptomyces sp001905445	87.7266	1687	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016755875.1	s__Streptomyces spororaveus	87.6762	1726	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642275.1	s__Streptomyces venezuelae_E	87.6425	1685	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	87.6308	1771	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014650695.1	s__Streptomyces avidinii	87.5602	1763	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000716685.1	s__Streptomyces virginiae_A	87.4271	1752	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003148825.1	s__Streptomyces sp003148825	87.4224	1741	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_014648795.1	s__Streptomyces cinnamonensis	87.412	1744	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
GCF_014650555.1	s__Streptomyces goshikiensis	86.9384	1726	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_018614195.1	s__Streptomyces sp018614195	86.9223	1666	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	86.7019	1746	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	81.6381	1074	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	81.2528	1360	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
GCF_014649115.1	s__Streptomyces eurythermus	81.0625	1350	2549	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001642695.1	s__Streptomyces chilikensis	80.9405	1142	2549	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	79.6216	1100	2549	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 10:51:55,686] [INFO] GTDB search result was written to GCF_014650935.1_ASM1465093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:55,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:55,691] [INFO] DFAST_QC result json was written to GCF_014650935.1_ASM1465093v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:55,691] [INFO] DFAST_QC completed!
[2024-01-24 10:51:55,691] [INFO] Total running time: 0h3m47s