[2024-01-25 18:05:50,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,455] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference
[2024-01-25 18:05:51,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,592] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,593] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc191fd5-5c18-4ee1-a055-0db198d4780e/GCF_000258595.1_Ssomaliensis1_genomic.fna.gz | prodigal -d GCF_000258595.1_Ssomaliensis1_genomic.fna/cds.fna -a GCF_000258595.1_Ssomaliensis1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:02,564] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:02,564] [INFO] Task started: HMMsearch
[2024-01-25 18:06:02,564] [INFO] Running command: hmmsearch --tblout GCF_000258595.1_Ssomaliensis1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/reference_markers.hmm GCF_000258595.1_Ssomaliensis1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:02,797] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:02,798] [INFO] Found 6/6 markers.
[2024-01-25 18:06:02,837] [INFO] Query marker FASTA was written to GCF_000258595.1_Ssomaliensis1_genomic.fna/markers.fasta
[2024-01-25 18:06:02,838] [INFO] Task started: Blastn
[2024-01-25 18:06:02,838] [INFO] Running command: blastn -query GCF_000258595.1_Ssomaliensis1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/reference_markers.fasta -out GCF_000258595.1_Ssomaliensis1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:04,161] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:04,165] [INFO] Selected 9 target genomes.
[2024-01-25 18:06:04,165] [INFO] Target genome list was writen to GCF_000258595.1_Ssomaliensis1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:04,172] [INFO] Task started: fastANI
[2024-01-25 18:06:04,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc191fd5-5c18-4ee1-a055-0db198d4780e/GCF_000258595.1_Ssomaliensis1_genomic.fna.gz --refList GCF_000258595.1_Ssomaliensis1_genomic.fna/target_genomes.txt --output GCF_000258595.1_Ssomaliensis1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:18,549] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:18,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:18,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:18,558] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:18,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:18,558] [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 sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	99.9332	1606	1606	95	conclusive
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	91.8333	1277	1606	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	90.7063	1292	1606	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	88.1193	1272	1606	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	88.0536	1254	1606	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	87.8304	867	1606	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.9379	1063	1606	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.8703	995	1606	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.7581	988	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:18,561] [INFO] DFAST Taxonomy check result was written to GCF_000258595.1_Ssomaliensis1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:18,562] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:18,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:18,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/checkm_data
[2024-01-25 18:06:18,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:18,625] [INFO] Task started: CheckM
[2024-01-25 18:06:18,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000258595.1_Ssomaliensis1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000258595.1_Ssomaliensis1_genomic.fna/checkm_input GCF_000258595.1_Ssomaliensis1_genomic.fna/checkm_result
[2024-01-25 18:07:12,060] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:12,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:12,083] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:12,083] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:12,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000258595.1_Ssomaliensis1_genomic.fna/markers.fasta)
[2024-01-25 18:07:12,084] [INFO] Task started: Blastn
[2024-01-25 18:07:12,084] [INFO] Running command: blastn -query GCF_000258595.1_Ssomaliensis1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9bbde2e-3828-4e10-b1de-9ad3ce48e790/dqc_reference/reference_markers_gtdb.fasta -out GCF_000258595.1_Ssomaliensis1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:14,253] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:14,255] [INFO] Selected 6 target genomes.
[2024-01-25 18:07:14,255] [INFO] Target genome list was writen to GCF_000258595.1_Ssomaliensis1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:14,276] [INFO] Task started: fastANI
[2024-01-25 18:07:14,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc191fd5-5c18-4ee1-a055-0db198d4780e/GCF_000258595.1_Ssomaliensis1_genomic.fna.gz --refList GCF_000258595.1_Ssomaliensis1_genomic.fna/target_genomes_gtdb.txt --output GCF_000258595.1_Ssomaliensis1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:24,470] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:24,475] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:24,475] [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
GCA_000258595.1	s__Streptomyces somaliensis_A	100.0	1595	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012396115.1	s__Streptomyces somaliensis	91.8025	1039	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	90.711	1291	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478605.2	s__Streptomyces thermolilacinus	88.7662	1236	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704425.1	s__Streptomyces fradiae	88.1009	1273	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_001426405.1	s__Streptomyces sp001426405	82.7812	1037	1606	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:24,478] [INFO] GTDB search result was written to GCF_000258595.1_Ssomaliensis1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:24,478] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:24,480] [INFO] DFAST_QC result json was written to GCF_000258595.1_Ssomaliensis1_genomic.fna/dqc_result.json
[2024-01-25 18:07:24,480] [INFO] DFAST_QC completed!
[2024-01-25 18:07:24,481] [INFO] Total running time: 0h1m34s