[2024-01-24 13:25:30,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,122] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference
[2024-01-24 13:25:31,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,444] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,444] [INFO] Running command: gunzip -c /var/lib/cwl/stgff3e2247-29a7-49c5-8e1c-e06d2bc98521/GCF_000720485.1_ASM72048v1_genomic.fna.gz | prodigal -d GCF_000720485.1_ASM72048v1_genomic.fna/cds.fna -a GCF_000720485.1_ASM72048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:54,918] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:54,919] [INFO] Task started: HMMsearch
[2024-01-24 13:25:54,919] [INFO] Running command: hmmsearch --tblout GCF_000720485.1_ASM72048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/reference_markers.hmm GCF_000720485.1_ASM72048v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:55,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:55,368] [INFO] Found 6/6 markers.
[2024-01-24 13:25:55,436] [INFO] Query marker FASTA was written to GCF_000720485.1_ASM72048v1_genomic.fna/markers.fasta
[2024-01-24 13:25:55,436] [INFO] Task started: Blastn
[2024-01-24 13:25:55,436] [INFO] Running command: blastn -query GCF_000720485.1_ASM72048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/reference_markers.fasta -out GCF_000720485.1_ASM72048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:56,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:56,728] [INFO] Selected 15 target genomes.
[2024-01-24 13:25:56,729] [INFO] Target genome list was writen to GCF_000720485.1_ASM72048v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:56,741] [INFO] Task started: fastANI
[2024-01-24 13:25:56,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgff3e2247-29a7-49c5-8e1c-e06d2bc98521/GCF_000720485.1_ASM72048v1_genomic.fna.gz --refList GCF_000720485.1_ASM72048v1_genomic.fna/target_genomes.txt --output GCF_000720485.1_ASM72048v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:26,656] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:26,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:26,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:26,680] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:26,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:26,681] [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 ochraceiscleroticus	strain=NRRL ISP-5594	GCA_000720485.1	47761	47761	type	True	100.0	2756	2761	95	conclusive
Streptomyces violens	strain=NRRL ISP-5597	GCA_000717745.1	66377	66377	type	True	94.9592	2287	2761	95	below_threshold
Streptomyces purpurogeneiscleroticus	strain=DSM 43156	GCA_020024005.1	68259	68259	type	True	94.5327	1990	2761	95	below_threshold
Streptomyces niger	strain=NRRL B-3857	GCA_000718305.1	66373	66373	type	True	90.0691	2094	2761	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	83.7606	1513	2761	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	83.6795	1421	2761	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.6124	1610	2761	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.5758	1601	2761	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.5671	1554	2761	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	83.5575	1546	2761	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.4938	1447	2761	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	83.4023	1175	2761	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	83.392	1493	2761	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	83.3784	1509	2761	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	83.1623	1507	2761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:26,682] [INFO] DFAST Taxonomy check result was written to GCF_000720485.1_ASM72048v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:26,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:26,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:26,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/checkm_data
[2024-01-24 13:26:26,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:26,764] [INFO] Task started: CheckM
[2024-01-24 13:26:26,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000720485.1_ASM72048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000720485.1_ASM72048v1_genomic.fna/checkm_input GCF_000720485.1_ASM72048v1_genomic.fna/checkm_result
[2024-01-24 13:27:48,022] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:48,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:48,081] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:48,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:48,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000720485.1_ASM72048v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:48,082] [INFO] Task started: Blastn
[2024-01-24 13:27:48,082] [INFO] Running command: blastn -query GCF_000720485.1_ASM72048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34518dbd-62e3-4c8c-abbf-00ba28a4cccf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000720485.1_ASM72048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:50,243] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:50,247] [INFO] Selected 6 target genomes.
[2024-01-24 13:27:50,247] [INFO] Target genome list was writen to GCF_000720485.1_ASM72048v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:50,262] [INFO] Task started: fastANI
[2024-01-24 13:27:50,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgff3e2247-29a7-49c5-8e1c-e06d2bc98521/GCF_000720485.1_ASM72048v1_genomic.fna.gz --refList GCF_000720485.1_ASM72048v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000720485.1_ASM72048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:05,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:05,050] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:05,051] [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_000720485.1	s__Streptomyces ochraceiscleroticus	100.0	2756	2761	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_000717745.1	s__Streptomyces violens	94.9592	2287	2761	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	90.8259	2070	2761	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	90.2433	2050	2761	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	90.0587	2096	2761	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	83.2814	1465	2761	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 13:28:05,052] [INFO] GTDB search result was written to GCF_000720485.1_ASM72048v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:05,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:05,056] [INFO] DFAST_QC result json was written to GCF_000720485.1_ASM72048v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:05,056] [INFO] DFAST_QC completed!
[2024-01-24 13:28:05,056] [INFO] Total running time: 0h2m35s