[2024-01-24 13:49:40,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference
[2024-01-24 13:49:41,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,324] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8acc60d-f1b3-4f7a-81aa-304f4c0e3ec4/GCF_017916255.1_ASM1791625v1_genomic.fna.gz | prodigal -d GCF_017916255.1_ASM1791625v1_genomic.fna/cds.fna -a GCF_017916255.1_ASM1791625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,116] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,116] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,117] [INFO] Running command: hmmsearch --tblout GCF_017916255.1_ASM1791625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/reference_markers.hmm GCF_017916255.1_ASM1791625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:04,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:04,450] [INFO] Found 6/6 markers.
[2024-01-24 13:50:04,513] [INFO] Query marker FASTA was written to GCF_017916255.1_ASM1791625v1_genomic.fna/markers.fasta
[2024-01-24 13:50:04,514] [INFO] Task started: Blastn
[2024-01-24 13:50:04,514] [INFO] Running command: blastn -query GCF_017916255.1_ASM1791625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/reference_markers.fasta -out GCF_017916255.1_ASM1791625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,868] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:05,868] [INFO] Target genome list was writen to GCF_017916255.1_ASM1791625v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:05,901] [INFO] Task started: fastANI
[2024-01-24 13:50:05,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8acc60d-f1b3-4f7a-81aa-304f4c0e3ec4/GCF_017916255.1_ASM1791625v1_genomic.fna.gz --refList GCF_017916255.1_ASM1791625v1_genomic.fna/target_genomes.txt --output GCF_017916255.1_ASM1791625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:42,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:42,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:42,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:42,488] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:42,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:42,488] [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 mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	100.0	2521	2524	95	conclusive
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	99.9137	2336	2524	95	conclusive
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	92.3186	1847	2524	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	85.803	1625	2524	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	84.2453	1321	2524	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	84.0209	1445	2524	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	83.9914	1449	2524	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	83.697	1417	2524	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	83.6342	1434	2524	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	83.5564	1478	2524	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	83.5116	1525	2524	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	83.4963	1497	2524	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	83.4279	1496	2524	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	83.3779	1498	2524	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	83.2415	1525	2524	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.7877	1345	2524	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.6626	1235	2524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:42,490] [INFO] DFAST Taxonomy check result was written to GCF_017916255.1_ASM1791625v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:42,491] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:42,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:42,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/checkm_data
[2024-01-24 13:50:42,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:42,559] [INFO] Task started: CheckM
[2024-01-24 13:50:42,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017916255.1_ASM1791625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017916255.1_ASM1791625v1_genomic.fna/checkm_input GCF_017916255.1_ASM1791625v1_genomic.fna/checkm_result
[2024-01-24 13:52:42,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:42,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:42,477] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:42,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:42,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017916255.1_ASM1791625v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:42,479] [INFO] Task started: Blastn
[2024-01-24 13:52:42,479] [INFO] Running command: blastn -query GCF_017916255.1_ASM1791625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8949737e-175d-4925-b4d2-8633e5811a49/dqc_reference/reference_markers_gtdb.fasta -out GCF_017916255.1_ASM1791625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:44,665] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:44,668] [INFO] Selected 12 target genomes.
[2024-01-24 13:52:44,668] [INFO] Target genome list was writen to GCF_017916255.1_ASM1791625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:44,755] [INFO] Task started: fastANI
[2024-01-24 13:52:44,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8acc60d-f1b3-4f7a-81aa-304f4c0e3ec4/GCF_017916255.1_ASM1791625v1_genomic.fna.gz --refList GCF_017916255.1_ASM1791625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017916255.1_ASM1791625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:10,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:10,905] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:10,905] [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_017916255.1	s__Streptomyces mobaraensis	100.0	2521	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	conclusive
GCF_014253015.1	s__Streptomyces sp014253015	94.4417	2114	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	88.842	1811	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999245.1	s__Streptomyces sp015999245	85.8975	1590	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187435.1	s__Streptomyces caatingaensis	85.7709	1630	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	84.2219	1324	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	83.5906	1474	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192455.1	s__Streptomyces albireticuli_B	83.5408	1542	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	83.5378	1433	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_002891295.1	s__Streptomyces eurocidicus	83.5053	1496	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_003011965.1	s__Streptomyces nondiastaticus	83.4888	1427	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	83.3998	1495	2524	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:10,907] [INFO] GTDB search result was written to GCF_017916255.1_ASM1791625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:10,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:10,911] [INFO] DFAST_QC result json was written to GCF_017916255.1_ASM1791625v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:10,911] [INFO] DFAST_QC completed!
[2024-01-24 13:53:10,912] [INFO] Total running time: 0h3m31s