[2024-01-25 18:59:35,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:35,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:35,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference
[2024-01-25 18:59:36,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:36,761] [INFO] Task started: Prodigal
[2024-01-25 18:59:36,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg69df0ff2-544d-4d00-836b-2a06e10072bb/GCF_017164735.1_ASM1716473v1_genomic.fna.gz | prodigal -d GCF_017164735.1_ASM1716473v1_genomic.fna/cds.fna -a GCF_017164735.1_ASM1716473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:53,280] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:53,280] [INFO] Task started: HMMsearch
[2024-01-25 18:59:53,280] [INFO] Running command: hmmsearch --tblout GCF_017164735.1_ASM1716473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/reference_markers.hmm GCF_017164735.1_ASM1716473v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:53,592] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:53,595] [INFO] Found 6/6 markers.
[2024-01-25 18:59:53,654] [INFO] Query marker FASTA was written to GCF_017164735.1_ASM1716473v1_genomic.fna/markers.fasta
[2024-01-25 18:59:53,654] [INFO] Task started: Blastn
[2024-01-25 18:59:53,654] [INFO] Running command: blastn -query GCF_017164735.1_ASM1716473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/reference_markers.fasta -out GCF_017164735.1_ASM1716473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:54,935] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:54,938] [INFO] Selected 12 target genomes.
[2024-01-25 18:59:54,938] [INFO] Target genome list was writen to GCF_017164735.1_ASM1716473v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:54,950] [INFO] Task started: fastANI
[2024-01-25 18:59:54,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg69df0ff2-544d-4d00-836b-2a06e10072bb/GCF_017164735.1_ASM1716473v1_genomic.fna.gz --refList GCF_017164735.1_ASM1716473v1_genomic.fna/target_genomes.txt --output GCF_017164735.1_ASM1716473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:20,607] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:20,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:20,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:20,617] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:00:20,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:20,617] [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
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	100.0	2180	2208	95	conclusive
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	99.9631	2191	2208	95	conclusive
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	89.2084	1606	2208	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	86.2944	1550	2208	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	84.179	1385	2208	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.6082	1380	2208	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.4208	1293	2208	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	83.1266	1391	2208	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.1855	962	2208	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	80.1465	1048	2208	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.9107	951	2208	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.5851	1079	2208	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:20,619] [INFO] DFAST Taxonomy check result was written to GCF_017164735.1_ASM1716473v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:20,620] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:20,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:20,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/checkm_data
[2024-01-25 19:00:20,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:20,692] [INFO] Task started: CheckM
[2024-01-25 19:00:20,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017164735.1_ASM1716473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017164735.1_ASM1716473v1_genomic.fna/checkm_input GCF_017164735.1_ASM1716473v1_genomic.fna/checkm_result
[2024-01-25 19:01:23,993] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:23,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:24,018] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:24,019] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:24,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017164735.1_ASM1716473v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:24,020] [INFO] Task started: Blastn
[2024-01-25 19:01:24,020] [INFO] Running command: blastn -query GCF_017164735.1_ASM1716473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg020b262a-e690-4cf3-b9b9-edaf214f7b1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017164735.1_ASM1716473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:26,229] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:26,233] [INFO] Selected 7 target genomes.
[2024-01-25 19:01:26,233] [INFO] Target genome list was writen to GCF_017164735.1_ASM1716473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:26,244] [INFO] Task started: fastANI
[2024-01-25 19:01:26,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg69df0ff2-544d-4d00-836b-2a06e10072bb/GCF_017164735.1_ASM1716473v1_genomic.fna.gz --refList GCF_017164735.1_ASM1716473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017164735.1_ASM1716473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:41,771] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:41,778] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:41,778] [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_016916835.1	s__Streptomyces bryophytorum	99.9631	2191	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCF_000701325.1	s__Streptomyces sp000701325	90.9455	1642	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	89.248	1601	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	86.3266	1545	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	86.2158	1530	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110255.1	s__Streptomyces rubidus	83.5922	1383	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783685.1	s__Streptomyces sp009783685	83.4825	906	2208	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:41,779] [INFO] GTDB search result was written to GCF_017164735.1_ASM1716473v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:41,780] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:41,782] [INFO] DFAST_QC result json was written to GCF_017164735.1_ASM1716473v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:41,782] [INFO] DFAST_QC completed!
[2024-01-25 19:01:41,783] [INFO] Total running time: 0h2m6s