[2024-01-24 11:43:40,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference
[2024-01-24 11:43:41,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:41,860] [INFO] Task started: Prodigal
[2024-01-24 11:43:41,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg5531e5cb-21d2-421b-99cc-f5b4f79c9764/GCF_020024005.1_ASM2002400v1_genomic.fna.gz | prodigal -d GCF_020024005.1_ASM2002400v1_genomic.fna/cds.fna -a GCF_020024005.1_ASM2002400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:01,264] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:01,264] [INFO] Task started: HMMsearch
[2024-01-24 11:44:01,264] [INFO] Running command: hmmsearch --tblout GCF_020024005.1_ASM2002400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/reference_markers.hmm GCF_020024005.1_ASM2002400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:01,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:01,877] [INFO] Found 6/6 markers.
[2024-01-24 11:44:01,941] [INFO] Query marker FASTA was written to GCF_020024005.1_ASM2002400v1_genomic.fna/markers.fasta
[2024-01-24 11:44:01,942] [INFO] Task started: Blastn
[2024-01-24 11:44:01,942] [INFO] Running command: blastn -query GCF_020024005.1_ASM2002400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/reference_markers.fasta -out GCF_020024005.1_ASM2002400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:03,302] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:03,306] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:03,306] [INFO] Target genome list was writen to GCF_020024005.1_ASM2002400v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:03,314] [INFO] Task started: fastANI
[2024-01-24 11:44:03,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5531e5cb-21d2-421b-99cc-f5b4f79c9764/GCF_020024005.1_ASM2002400v1_genomic.fna.gz --refList GCF_020024005.1_ASM2002400v1_genomic.fna/target_genomes.txt --output GCF_020024005.1_ASM2002400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:31,390] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:31,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:31,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:31,402] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:31,402] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:31,402] [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 purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	100.0	2309	2333	95	inconclusive
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	95.4903	1961	2333	95	inconclusive
Streptomyces ochraceiscleroticus	strain=NRRL ISP-5594	GCA_000720485.1	47761	47761	type	True	94.6317	2002	2333	95	below_threshold
Streptomyces niger	strain=NRRL B-3857	GCA_000718305.1	66373	66373	type	True	90.0686	1818	2333	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	83.8783	1329	2333	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.7861	1413	2333	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	83.6822	1411	2333	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	83.5664	1371	2333	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.526	1384	2333	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	83.4423	1243	2333	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.3897	1299	2333	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	83.3743	1323	2333	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	83.3342	1054	2333	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.1597	1151	2333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:31,404] [INFO] DFAST Taxonomy check result was written to GCF_020024005.1_ASM2002400v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:31,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:31,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:31,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/checkm_data
[2024-01-24 11:44:31,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:31,483] [INFO] Task started: CheckM
[2024-01-24 11:44:31,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020024005.1_ASM2002400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020024005.1_ASM2002400v1_genomic.fna/checkm_input GCF_020024005.1_ASM2002400v1_genomic.fna/checkm_result
[2024-01-24 11:45:33,731] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:33,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:33,760] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:33,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:33,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020024005.1_ASM2002400v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:33,761] [INFO] Task started: Blastn
[2024-01-24 11:45:33,762] [INFO] Running command: blastn -query GCF_020024005.1_ASM2002400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg048e0549-8dfc-46ee-b426-63cff34ff1c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_020024005.1_ASM2002400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:35,852] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:35,857] [INFO] Selected 6 target genomes.
[2024-01-24 11:45:35,857] [INFO] Target genome list was writen to GCF_020024005.1_ASM2002400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:35,863] [INFO] Task started: fastANI
[2024-01-24 11:45:35,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg5531e5cb-21d2-421b-99cc-f5b4f79c9764/GCF_020024005.1_ASM2002400v1_genomic.fna.gz --refList GCF_020024005.1_ASM2002400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020024005.1_ASM2002400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:48,641] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:48,653] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:48,653] [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_000717745.1	s__Streptomyces violens	95.4819	1961	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0121	N/A	N/A	N/A	N/A	1	conclusive
GCF_000720485.1	s__Streptomyces ochraceiscleroticus	94.6317	2002	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0121	N/A	N/A	N/A	N/A	1	-
GCA_000720555.1	s__Streptomyces sclerotialus	90.8353	1823	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920575.1	s__Streptomyces sp002920575	90.3406	1783	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718305.1	s__Streptomyces niger	90.0278	1823	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	83.2766	1293	2333	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:48,655] [INFO] GTDB search result was written to GCF_020024005.1_ASM2002400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:48,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:48,658] [INFO] DFAST_QC result json was written to GCF_020024005.1_ASM2002400v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:48,658] [INFO] DFAST_QC completed!
[2024-01-24 11:45:48,658] [INFO] Total running time: 0h2m8s