[2024-01-24 13:55:40,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference
[2024-01-24 13:55:41,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:41,903] [INFO] Task started: Prodigal
[2024-01-24 13:55:41,904] [INFO] Running command: gunzip -c /var/lib/cwl/stga7344a34-da2a-4ae6-9baf-8ec916c9872e/GCF_014650695.1_ASM1465069v1_genomic.fna.gz | prodigal -d GCF_014650695.1_ASM1465069v1_genomic.fna/cds.fna -a GCF_014650695.1_ASM1465069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:07,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:07,940] [INFO] Task started: HMMsearch
[2024-01-24 13:56:07,940] [INFO] Running command: hmmsearch --tblout GCF_014650695.1_ASM1465069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/reference_markers.hmm GCF_014650695.1_ASM1465069v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:08,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:08,384] [INFO] Found 6/6 markers.
[2024-01-24 13:56:08,447] [INFO] Query marker FASTA was written to GCF_014650695.1_ASM1465069v1_genomic.fna/markers.fasta
[2024-01-24 13:56:08,448] [INFO] Task started: Blastn
[2024-01-24 13:56:08,448] [INFO] Running command: blastn -query GCF_014650695.1_ASM1465069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/reference_markers.fasta -out GCF_014650695.1_ASM1465069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:09,673] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:09,676] [INFO] Selected 15 target genomes.
[2024-01-24 13:56:09,676] [INFO] Target genome list was writen to GCF_014650695.1_ASM1465069v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:09,729] [INFO] Task started: fastANI
[2024-01-24 13:56:09,730] [INFO] Running command: fastANI --query /var/lib/cwl/stga7344a34-da2a-4ae6-9baf-8ec916c9872e/GCF_014650695.1_ASM1465069v1_genomic.fna.gz --refList GCF_014650695.1_ASM1465069v1_genomic.fna/target_genomes.txt --output GCF_014650695.1_ASM1465069v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:40,502] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:40,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:40,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:40,518] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:40,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:40,519] [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 avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	100.0	2751	2752	95	conclusive
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	99.9934	2742	2752	95	conclusive
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	92.1859	2207	2752	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	92.1809	2229	2752	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	91.9718	2164	2752	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	89.4066	2074	2752	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	89.0477	1931	2752	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	88.1295	1986	2752	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	88.0402	1976	2752	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	87.6548	1781	2752	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.7975	1358	2752	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.4113	1002	2752	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.2979	1043	2752	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.0827	1161	2752	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	80.8323	1174	2752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:40,521] [INFO] DFAST Taxonomy check result was written to GCF_014650695.1_ASM1465069v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:40,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:40,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:40,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/checkm_data
[2024-01-24 13:56:40,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:40,603] [INFO] Task started: CheckM
[2024-01-24 13:56:40,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650695.1_ASM1465069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650695.1_ASM1465069v1_genomic.fna/checkm_input GCF_014650695.1_ASM1465069v1_genomic.fna/checkm_result
[2024-01-24 13:58:40,448] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:40,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:40,481] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:40,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:40,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650695.1_ASM1465069v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:40,483] [INFO] Task started: Blastn
[2024-01-24 13:58:40,483] [INFO] Running command: blastn -query GCF_014650695.1_ASM1465069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecdbb12f-a993-4545-b34c-f2b1dd025f01/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650695.1_ASM1465069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:42,654] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:42,659] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:42,659] [INFO] Target genome list was writen to GCF_014650695.1_ASM1465069v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:42,669] [INFO] Task started: fastANI
[2024-01-24 13:58:42,669] [INFO] Running command: fastANI --query /var/lib/cwl/stga7344a34-da2a-4ae6-9baf-8ec916c9872e/GCF_014650695.1_ASM1465069v1_genomic.fna.gz --refList GCF_014650695.1_ASM1465069v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650695.1_ASM1465069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:06,367] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,378] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:06,378] [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_014650695.1	s__Streptomyces avidinii	100.0	2751	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002080455.1	s__Streptomyces sp002080455	94.5488	2287	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_017639205.1	s__Streptomyces nojiriensis	92.1473	2233	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016755875.1	s__Streptomyces spororaveus	91.9359	2170	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	91.8017	2242	2752	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	91.7182	2235	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_008642275.1	s__Streptomyces venezuelae_E	91.6977	2106	2752	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	90.2449	2040	2752	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	88.0247	1978	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,380] [INFO] GTDB search result was written to GCF_014650695.1_ASM1465069v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:06,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:06,385] [INFO] DFAST_QC result json was written to GCF_014650695.1_ASM1465069v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:06,386] [INFO] DFAST_QC completed!
[2024-01-24 13:59:06,386] [INFO] Total running time: 0h3m26s