[2024-01-24 15:26:50,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:50,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:50,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference
[2024-01-24 15:26:52,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:52,911] [INFO] Task started: Prodigal
[2024-01-24 15:26:52,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg9417c276-2047-4905-9fbd-54b86a5cd9bd/GCF_016741935.1_ASM1674193v1_genomic.fna.gz | prodigal -d GCF_016741935.1_ASM1674193v1_genomic.fna/cds.fna -a GCF_016741935.1_ASM1674193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:53,432] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:53,433] [INFO] Task started: HMMsearch
[2024-01-24 15:27:53,433] [INFO] Running command: hmmsearch --tblout GCF_016741935.1_ASM1674193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/reference_markers.hmm GCF_016741935.1_ASM1674193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:53,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:53,860] [INFO] Found 6/6 markers.
[2024-01-24 15:27:53,957] [INFO] Query marker FASTA was written to GCF_016741935.1_ASM1674193v1_genomic.fna/markers.fasta
[2024-01-24 15:27:53,957] [INFO] Task started: Blastn
[2024-01-24 15:27:53,957] [INFO] Running command: blastn -query GCF_016741935.1_ASM1674193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/reference_markers.fasta -out GCF_016741935.1_ASM1674193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:55,237] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:55,240] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:55,240] [INFO] Target genome list was writen to GCF_016741935.1_ASM1674193v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:55,244] [INFO] Task started: fastANI
[2024-01-24 15:27:55,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg9417c276-2047-4905-9fbd-54b86a5cd9bd/GCF_016741935.1_ASM1674193v1_genomic.fna.gz --refList GCF_016741935.1_ASM1674193v1_genomic.fna/target_genomes.txt --output GCF_016741935.1_ASM1674193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:45,271] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:45,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:45,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:45,283] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:28:45,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:28:45,283] [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 iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	94.9901	3104	4279	95	below_threshold
Streptomyces rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	94.8498	3170	4279	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	94.8453	3172	4279	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	94.8311	3194	4279	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	94.7853	3200	4279	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	94.2964	2338	4279	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	93.9376	2349	4279	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	92.3609	2897	4279	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	92.0294	2926	4279	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.9669	1491	4279	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.8815	1600	4279	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.7924	1517	4279	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.176	1368	4279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:45,285] [INFO] DFAST Taxonomy check result was written to GCF_016741935.1_ASM1674193v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:45,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:45,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:45,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/checkm_data
[2024-01-24 15:28:45,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:45,396] [INFO] Task started: CheckM
[2024-01-24 15:28:45,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016741935.1_ASM1674193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016741935.1_ASM1674193v1_genomic.fna/checkm_input GCF_016741935.1_ASM1674193v1_genomic.fna/checkm_result
[2024-01-24 15:32:17,645] [INFO] Task succeeded: CheckM
[2024-01-24 15:32:17,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:32:17,671] [INFO] ===== Completeness check finished =====
[2024-01-24 15:32:17,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:32:17,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016741935.1_ASM1674193v1_genomic.fna/markers.fasta)
[2024-01-24 15:32:17,672] [INFO] Task started: Blastn
[2024-01-24 15:32:17,672] [INFO] Running command: blastn -query GCF_016741935.1_ASM1674193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7f9e97-2760-420d-862f-65a725ef5209/dqc_reference/reference_markers_gtdb.fasta -out GCF_016741935.1_ASM1674193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:19,725] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:19,728] [INFO] Selected 10 target genomes.
[2024-01-24 15:32:19,728] [INFO] Target genome list was writen to GCF_016741935.1_ASM1674193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:32:19,757] [INFO] Task started: fastANI
[2024-01-24 15:32:19,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg9417c276-2047-4905-9fbd-54b86a5cd9bd/GCF_016741935.1_ASM1674193v1_genomic.fna.gz --refList GCF_016741935.1_ASM1674193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016741935.1_ASM1674193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:04,575] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:04,598] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:04,598] [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_016741935.1	s__Streptomyces sp016741935	100.0	4273	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874715.1	s__Streptomyces iranensis	94.9972	3104	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_003675955.1	s__Streptomyces rapamycinicus	94.8573	3190	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	-
GCF_018138715.1	s__Streptomyces asiaticus	94.8327	3061	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCA_005405945.1	s__Streptomyces violaceusniger	94.3219	2953	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_000968685.2	s__Streptomyces antioxidans	93.5407	2486	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069625.1	s__Streptomyces yatensis	92.3944	2892	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_005405925.1	s__Streptomyces antimycoticus	92.0598	2921	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCF_015689475.1	s__Streptomyces solisilvae	92.0024	2990	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCF_000147815.2	s__Streptomyces violaceusniger_A	91.9708	2878	4279	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:04,599] [INFO] GTDB search result was written to GCF_016741935.1_ASM1674193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:04,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:04,603] [INFO] DFAST_QC result json was written to GCF_016741935.1_ASM1674193v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:04,603] [INFO] DFAST_QC completed!
[2024-01-24 15:33:04,603] [INFO] Total running time: 0h6m14s