[2024-01-24 14:21:44,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:44,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:44,050] [INFO] DQC Reference Directory: /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference
[2024-01-24 14:21:45,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:45,243] [INFO] Task started: Prodigal
[2024-01-24 14:21:45,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b3e7779-b201-45ec-bbe4-f129c1754bce/GCF_012396115.1_ASM1239611v1_genomic.fna.gz | prodigal -d GCF_012396115.1_ASM1239611v1_genomic.fna/cds.fna -a GCF_012396115.1_ASM1239611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:21:55,761] [INFO] Task succeeded: Prodigal
[2024-01-24 14:21:55,762] [INFO] Task started: HMMsearch
[2024-01-24 14:21:55,762] [INFO] Running command: hmmsearch --tblout GCF_012396115.1_ASM1239611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/reference_markers.hmm GCF_012396115.1_ASM1239611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:21:56,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:21:56,035] [INFO] Found 6/6 markers.
[2024-01-24 14:21:56,074] [INFO] Query marker FASTA was written to GCF_012396115.1_ASM1239611v1_genomic.fna/markers.fasta
[2024-01-24 14:21:56,075] [INFO] Task started: Blastn
[2024-01-24 14:21:56,075] [INFO] Running command: blastn -query GCF_012396115.1_ASM1239611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/reference_markers.fasta -out GCF_012396115.1_ASM1239611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:57,425] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:57,429] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:57,429] [INFO] Target genome list was writen to GCF_012396115.1_ASM1239611v1_genomic.fna/target_genomes.txt
[2024-01-24 14:21:57,447] [INFO] Task started: fastANI
[2024-01-24 14:21:57,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3e7779-b201-45ec-bbe4-f129c1754bce/GCF_012396115.1_ASM1239611v1_genomic.fna.gz --refList GCF_012396115.1_ASM1239611v1_genomic.fna/target_genomes.txt --output GCF_012396115.1_ASM1239611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:11,479] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:11,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:11,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:11,494] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:11,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:11,494] [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	99.832	1273	1304	95	conclusive
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	92.0271	1097	1304	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	91.2273	1066	1304	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	88.5928	1051	1304	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	88.546	1075	1304	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	88.243	770	1304	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.3731	913	1304	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.1747	876	1304	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.2902	830	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:11,496] [INFO] DFAST Taxonomy check result was written to GCF_012396115.1_ASM1239611v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:11,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:11,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:11,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/checkm_data
[2024-01-24 14:22:11,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:11,549] [INFO] Task started: CheckM
[2024-01-24 14:22:11,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396115.1_ASM1239611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396115.1_ASM1239611v1_genomic.fna/checkm_input GCF_012396115.1_ASM1239611v1_genomic.fna/checkm_result
[2024-01-24 14:22:48,979] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:48,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.81%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,010] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:49,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:49,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396115.1_ASM1239611v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:49,012] [INFO] Task started: Blastn
[2024-01-24 14:22:49,012] [INFO] Running command: blastn -query GCF_012396115.1_ASM1239611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08ea891-213b-46be-8b17-9c64e766fef9/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396115.1_ASM1239611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:51,232] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:51,235] [INFO] Selected 6 target genomes.
[2024-01-24 14:22:51,235] [INFO] Target genome list was writen to GCF_012396115.1_ASM1239611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:51,243] [INFO] Task started: fastANI
[2024-01-24 14:22:51,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3e7779-b201-45ec-bbe4-f129c1754bce/GCF_012396115.1_ASM1239611v1_genomic.fna.gz --refList GCF_012396115.1_ASM1239611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396115.1_ASM1239611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:59,936] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:59,948] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:59,949] [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	100.0	1280	1304	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	92.0031	1044	1304	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	91.1959	1068	1304	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	89.1314	1047	1304	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	88.5567	1075	1304	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	83.3242	916	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,951] [INFO] GTDB search result was written to GCF_012396115.1_ASM1239611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:59,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:59,956] [INFO] DFAST_QC result json was written to GCF_012396115.1_ASM1239611v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:59,956] [INFO] DFAST_QC completed!
[2024-01-24 14:22:59,956] [INFO] Total running time: 0h1m16s