[2024-01-25 17:54:35,940] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference
[2024-01-25 17:54:37,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:37,180] [INFO] Task started: Prodigal
[2024-01-25 17:54:37,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg2654e626-d326-4bde-8228-447513d0050b/GCF_030161855.1_ASM3016185v1_genomic.fna.gz | prodigal -d GCF_030161855.1_ASM3016185v1_genomic.fna/cds.fna -a GCF_030161855.1_ASM3016185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:56,633] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:56,633] [INFO] Task started: HMMsearch
[2024-01-25 17:54:56,633] [INFO] Running command: hmmsearch --tblout GCF_030161855.1_ASM3016185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/reference_markers.hmm GCF_030161855.1_ASM3016185v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:56,780] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:56,781] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg2654e626-d326-4bde-8228-447513d0050b/GCF_030161855.1_ASM3016185v1_genomic.fna.gz]
[2024-01-25 17:54:56,815] [INFO] Query marker FASTA was written to GCF_030161855.1_ASM3016185v1_genomic.fna/markers.fasta
[2024-01-25 17:54:56,815] [INFO] Task started: Blastn
[2024-01-25 17:54:56,815] [INFO] Running command: blastn -query GCF_030161855.1_ASM3016185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/reference_markers.fasta -out GCF_030161855.1_ASM3016185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:57,324] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:57,326] [INFO] Selected 5 target genomes.
[2024-01-25 17:54:57,326] [INFO] Target genome list was writen to GCF_030161855.1_ASM3016185v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:57,328] [INFO] Task started: fastANI
[2024-01-25 17:54:57,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg2654e626-d326-4bde-8228-447513d0050b/GCF_030161855.1_ASM3016185v1_genomic.fna.gz --refList GCF_030161855.1_ASM3016185v1_genomic.fna/target_genomes.txt --output GCF_030161855.1_ASM3016185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:04,164] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:04,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:04,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:04,170] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:04,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:04,170] [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 galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	76.7898	544	1304	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	76.7164	544	1304	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	76.6775	551	1304	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	76.6197	546	1304	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	76.5672	474	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:04,171] [INFO] DFAST Taxonomy check result was written to GCF_030161855.1_ASM3016185v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:04,172] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:04,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:04,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/checkm_data
[2024-01-25 17:55:04,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:04,212] [INFO] Task started: CheckM
[2024-01-25 17:55:04,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161855.1_ASM3016185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161855.1_ASM3016185v1_genomic.fna/checkm_input GCF_030161855.1_ASM3016185v1_genomic.fna/checkm_result
[2024-01-25 17:56:02,967] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:02,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:02,989] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:02,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:02,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161855.1_ASM3016185v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:02,990] [INFO] Task started: Blastn
[2024-01-25 17:56:02,991] [INFO] Running command: blastn -query GCF_030161855.1_ASM3016185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f83d4c8-5600-4bb9-ad1e-4c54d38687e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161855.1_ASM3016185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:03,529] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:03,533] [INFO] Selected 5 target genomes.
[2024-01-25 17:56:03,533] [INFO] Target genome list was writen to GCF_030161855.1_ASM3016185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:03,547] [INFO] Task started: fastANI
[2024-01-25 17:56:03,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg2654e626-d326-4bde-8228-447513d0050b/GCF_030161855.1_ASM3016185v1_genomic.fna.gz --refList GCF_030161855.1_ASM3016185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161855.1_ASM3016185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:10,696] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:10,700] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:56:10,700] [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_001426435.1	s__Angustibacter sp001426435	80.5564	701	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Angustibacteraceae;g__Angustibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139625.1	s__Actinospica sp018139625	76.84	493	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103985.1	s__Streptomyces guanduensis	76.654	536	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258605.2	s__Streptomyces_D bronchialis	76.5546	477	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813365.1	s__Kitasatospora sp002813365	76.538	600	1304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:10,703] [INFO] GTDB search result was written to GCF_030161855.1_ASM3016185v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:10,703] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:10,705] [INFO] DFAST_QC result json was written to GCF_030161855.1_ASM3016185v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:10,705] [INFO] DFAST_QC completed!
[2024-01-25 17:56:10,705] [INFO] Total running time: 0h1m35s