[2024-01-24 12:06:14,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference
[2024-01-24 12:06:16,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,186] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc337638-c4dd-43d5-aa0e-936939e4909d/GCF_013410345.1_ASM1341034v1_genomic.fna.gz | prodigal -d GCF_013410345.1_ASM1341034v1_genomic.fna/cds.fna -a GCF_013410345.1_ASM1341034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:34,779] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:34,779] [INFO] Task started: HMMsearch
[2024-01-24 12:06:34,779] [INFO] Running command: hmmsearch --tblout GCF_013410345.1_ASM1341034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/reference_markers.hmm GCF_013410345.1_ASM1341034v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,153] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,214] [INFO] Query marker FASTA was written to GCF_013410345.1_ASM1341034v1_genomic.fna/markers.fasta
[2024-01-24 12:06:35,215] [INFO] Task started: Blastn
[2024-01-24 12:06:35,215] [INFO] Running command: blastn -query GCF_013410345.1_ASM1341034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/reference_markers.fasta -out GCF_013410345.1_ASM1341034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,868] [INFO] Selected 10 target genomes.
[2024-01-24 12:06:36,869] [INFO] Target genome list was writen to GCF_013410345.1_ASM1341034v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:36,875] [INFO] Task started: fastANI
[2024-01-24 12:06:36,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc337638-c4dd-43d5-aa0e-936939e4909d/GCF_013410345.1_ASM1341034v1_genomic.fna.gz --refList GCF_013410345.1_ASM1341034v1_genomic.fna/target_genomes.txt --output GCF_013410345.1_ASM1341034v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:55,793] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:55,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:55,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:55,803] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:55,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:55,803] [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
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	100.0	1925	1927	95	conclusive
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	89.7591	1641	1927	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	88.4519	1578	1927	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	88.3421	1580	1927	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	85.1342	1446	1927	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	85.0705	1479	1927	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	85.0563	1259	1927	95	below_threshold
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	84.3369	1302	1927	95	below_threshold
Saccharopolyspora terrae	strain=16K309	GCA_004348435.1	2530384	2530384	type	True	83.3432	1228	1927	95	below_threshold
Saccharopolyspora endophytica	strain=KCTC 19397	GCA_018070075.1	543886	543886	type	True	83.2905	1238	1927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:55,805] [INFO] DFAST Taxonomy check result was written to GCF_013410345.1_ASM1341034v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:55,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:55,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:55,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/checkm_data
[2024-01-24 12:06:55,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:55,866] [INFO] Task started: CheckM
[2024-01-24 12:06:55,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410345.1_ASM1341034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410345.1_ASM1341034v1_genomic.fna/checkm_input GCF_013410345.1_ASM1341034v1_genomic.fna/checkm_result
[2024-01-24 12:09:08,550] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:08,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:08,576] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:08,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:08,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410345.1_ASM1341034v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:08,577] [INFO] Task started: Blastn
[2024-01-24 12:09:08,577] [INFO] Running command: blastn -query GCF_013410345.1_ASM1341034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg968417b4-59f0-4ef6-aa52-dce2cc704015/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410345.1_ASM1341034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:10,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:10,992] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:10,992] [INFO] Target genome list was writen to GCF_013410345.1_ASM1341034v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:11,003] [INFO] Task started: fastANI
[2024-01-24 12:09:11,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc337638-c4dd-43d5-aa0e-936939e4909d/GCF_013410345.1_ASM1341034v1_genomic.fna.gz --refList GCF_013410345.1_ASM1341034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410345.1_ASM1341034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:29,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:29,454] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:29,454] [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_013410345.1	s__Saccharopolyspora hordei	100.0	1924	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008630535.1	s__Saccharopolyspora hirsuta	89.7859	1638	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	88.4407	1579	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_900112555.1	s__Saccharopolyspora jiangxiensis	88.3559	1583	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	99.99	1.00	1.00	3	-
GCF_004348985.1	s__Saccharopolyspora sp004348985	85.1101	1450	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106995.1	s__Saccharopolyspora shandongensis	85.0811	1478	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	85.0359	1262	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697215.1	s__Saccharopolyspora pogona	84.5114	1307	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	95.67	95.67	0.80	0.80	2	-
GCF_000194155.1	s__Saccharopolyspora spinosa	84.3963	1294	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.78	99.78	0.99	0.98	3	-
GCF_018070075.1	s__Saccharopolyspora endophytica	83.2548	1243	1927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	96.33	95.95	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:29,457] [INFO] GTDB search result was written to GCF_013410345.1_ASM1341034v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:29,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:29,460] [INFO] DFAST_QC result json was written to GCF_013410345.1_ASM1341034v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:29,461] [INFO] DFAST_QC completed!
[2024-01-24 12:09:29,461] [INFO] Total running time: 0h3m15s