[2024-01-24 11:12:48,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference
[2024-01-24 11:12:49,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,914] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,914] [INFO] Running command: gunzip -c /var/lib/cwl/stg3342dd17-d0fd-49c0-b3a0-a40c32b9b010/GCF_000331185.2_ASM33118v2_genomic.fna.gz | prodigal -d GCF_000331185.2_ASM33118v2_genomic.fna/cds.fna -a GCF_000331185.2_ASM33118v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:19,763] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:19,763] [INFO] Task started: HMMsearch
[2024-01-24 11:13:19,764] [INFO] Running command: hmmsearch --tblout GCF_000331185.2_ASM33118v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/reference_markers.hmm GCF_000331185.2_ASM33118v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:20,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:20,153] [INFO] Found 6/6 markers.
[2024-01-24 11:13:20,225] [INFO] Query marker FASTA was written to GCF_000331185.2_ASM33118v2_genomic.fna/markers.fasta
[2024-01-24 11:13:20,225] [INFO] Task started: Blastn
[2024-01-24 11:13:20,225] [INFO] Running command: blastn -query GCF_000331185.2_ASM33118v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/reference_markers.fasta -out GCF_000331185.2_ASM33118v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:21,550] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:21,554] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:21,555] [INFO] Target genome list was writen to GCF_000331185.2_ASM33118v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:21,564] [INFO] Task started: fastANI
[2024-01-24 11:13:21,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg3342dd17-d0fd-49c0-b3a0-a40c32b9b010/GCF_000331185.2_ASM33118v2_genomic.fna.gz --refList GCF_000331185.2_ASM33118v2_genomic.fna/target_genomes.txt --output GCF_000331185.2_ASM33118v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:47,221] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:47,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:47,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:47,235] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:13:47,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:47,235] [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 rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	100.0	3212	3214	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	99.9974	3213	3214	95	conclusive
Streptomyces rimosus	strain=ATCC 10970	GCA_008704655.1	1927	1927	type	True	99.9939	3114	3214	95	conclusive
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	99.9694	3140	3214	95	conclusive
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	94.0664	2643	3214	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	89.6663	2354	3214	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	89.6628	2430	3214	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.9318	1553	3214	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.9706	1588	3214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:47,237] [INFO] DFAST Taxonomy check result was written to GCF_000331185.2_ASM33118v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:47,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:47,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:47,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/checkm_data
[2024-01-24 11:13:47,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:47,324] [INFO] Task started: CheckM
[2024-01-24 11:13:47,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331185.2_ASM33118v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331185.2_ASM33118v2_genomic.fna/checkm_input GCF_000331185.2_ASM33118v2_genomic.fna/checkm_result
[2024-01-24 11:15:57,740] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:57,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:57,770] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:57,771] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:57,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331185.2_ASM33118v2_genomic.fna/markers.fasta)
[2024-01-24 11:15:57,772] [INFO] Task started: Blastn
[2024-01-24 11:15:57,772] [INFO] Running command: blastn -query GCF_000331185.2_ASM33118v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e82aaea-2424-4c1c-b836-ff76fa4dd38c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331185.2_ASM33118v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:59,917] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:59,921] [INFO] Selected 6 target genomes.
[2024-01-24 11:15:59,921] [INFO] Target genome list was writen to GCF_000331185.2_ASM33118v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:59,983] [INFO] Task started: fastANI
[2024-01-24 11:15:59,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg3342dd17-d0fd-49c0-b3a0-a40c32b9b010/GCF_000331185.2_ASM33118v2_genomic.fna.gz --refList GCF_000331185.2_ASM33118v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000331185.2_ASM33118v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:17,270] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:17,281] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:17,281] [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_008704655.1	s__Streptomyces rimosus	99.9798	3117	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	conclusive
GCF_008634025.1	s__Streptomyces albofaciens	94.0762	2642	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720725.1	s__Streptomyces rimosus_A	93.8729	2593	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905005.1	s__Streptomyces sp001905005	89.9691	2445	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865135.1	s__Streptomyces chrestomyceticus	89.8596	2441	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
GCF_000715845.1	s__Streptomyces monomycini	89.6999	2285	3214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:17,283] [INFO] GTDB search result was written to GCF_000331185.2_ASM33118v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:17,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:17,287] [INFO] DFAST_QC result json was written to GCF_000331185.2_ASM33118v2_genomic.fna/dqc_result.json
[2024-01-24 11:16:17,287] [INFO] DFAST_QC completed!
[2024-01-24 11:16:17,287] [INFO] Total running time: 0h3m29s