[2024-01-25 18:42:50,848] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference
[2024-01-25 18:42:51,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,967] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,967] [INFO] Running command: gunzip -c /var/lib/cwl/stga47be28e-149e-4104-9ce0-512d51f416b0/GCF_024349285.1_ASM2434928v1_genomic.fna.gz | prodigal -d GCF_024349285.1_ASM2434928v1_genomic.fna/cds.fna -a GCF_024349285.1_ASM2434928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:03,552] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:03,552] [INFO] Task started: HMMsearch
[2024-01-25 18:43:03,552] [INFO] Running command: hmmsearch --tblout GCF_024349285.1_ASM2434928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/reference_markers.hmm GCF_024349285.1_ASM2434928v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:03,844] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:03,845] [INFO] Found 6/6 markers.
[2024-01-25 18:43:03,886] [INFO] Query marker FASTA was written to GCF_024349285.1_ASM2434928v1_genomic.fna/markers.fasta
[2024-01-25 18:43:03,886] [INFO] Task started: Blastn
[2024-01-25 18:43:03,886] [INFO] Running command: blastn -query GCF_024349285.1_ASM2434928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/reference_markers.fasta -out GCF_024349285.1_ASM2434928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:05,199] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:05,202] [INFO] Selected 9 target genomes.
[2024-01-25 18:43:05,202] [INFO] Target genome list was writen to GCF_024349285.1_ASM2434928v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:05,212] [INFO] Task started: fastANI
[2024-01-25 18:43:05,212] [INFO] Running command: fastANI --query /var/lib/cwl/stga47be28e-149e-4104-9ce0-512d51f416b0/GCF_024349285.1_ASM2434928v1_genomic.fna.gz --refList GCF_024349285.1_ASM2434928v1_genomic.fna/target_genomes.txt --output GCF_024349285.1_ASM2434928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:20,932] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:20,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:20,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:20,941] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:20,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:20,942] [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 somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	100.0	1648	1648	95	conclusive
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	91.9433	1362	1648	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	91.0952	1331	1648	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	88.4778	1330	1648	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	88.4149	1302	1648	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	88.1142	875	1648	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.0232	1108	1648	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.9123	1064	1648	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.0753	970	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:20,943] [INFO] DFAST Taxonomy check result was written to GCF_024349285.1_ASM2434928v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:20,944] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:20,944] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:20,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/checkm_data
[2024-01-25 18:43:20,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:20,993] [INFO] Task started: CheckM
[2024-01-25 18:43:20,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024349285.1_ASM2434928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024349285.1_ASM2434928v1_genomic.fna/checkm_input GCF_024349285.1_ASM2434928v1_genomic.fna/checkm_result
[2024-01-25 18:44:24,135] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:24,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:24,155] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:24,155] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:24,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024349285.1_ASM2434928v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:24,156] [INFO] Task started: Blastn
[2024-01-25 18:44:24,156] [INFO] Running command: blastn -query GCF_024349285.1_ASM2434928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c5a55ed-31a5-47e1-8758-d97434ef409f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024349285.1_ASM2434928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:26,342] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:26,345] [INFO] Selected 6 target genomes.
[2024-01-25 18:44:26,345] [INFO] Target genome list was writen to GCF_024349285.1_ASM2434928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:26,349] [INFO] Task started: fastANI
[2024-01-25 18:44:26,349] [INFO] Running command: fastANI --query /var/lib/cwl/stga47be28e-149e-4104-9ce0-512d51f416b0/GCF_024349285.1_ASM2434928v1_genomic.fna.gz --refList GCF_024349285.1_ASM2434928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024349285.1_ASM2434928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:36,360] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:36,365] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:36,366] [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_012396115.1	s__Streptomyces somaliensis	99.5649	1248	1648	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_000258595.1	s__Streptomyces somaliensis_A	91.8605	1276	1648	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	91.0665	1334	1648	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	88.8769	1309	1648	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	88.4699	1333	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_012927245.1	s__Streptomyces sp012927245	83.1794	1083	1648	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 18:44:36,367] [INFO] GTDB search result was written to GCF_024349285.1_ASM2434928v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:36,368] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:36,371] [INFO] DFAST_QC result json was written to GCF_024349285.1_ASM2434928v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:36,371] [INFO] DFAST_QC completed!
[2024-01-25 18:44:36,371] [INFO] Total running time: 0h1m46s