[2024-01-25 17:54:50,661] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:50,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:50,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference
[2024-01-25 17:54:51,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:51,834] [INFO] Task started: Prodigal
[2024-01-25 17:54:51,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg20a8faa8-89ad-4d0e-b3d6-f7135825cfd7/GCF_014384705.1_ASM1438470v1_genomic.fna.gz | prodigal -d GCF_014384705.1_ASM1438470v1_genomic.fna/cds.fna -a GCF_014384705.1_ASM1438470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:59,145] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:59,145] [INFO] Task started: HMMsearch
[2024-01-25 17:54:59,145] [INFO] Running command: hmmsearch --tblout GCF_014384705.1_ASM1438470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/reference_markers.hmm GCF_014384705.1_ASM1438470v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:59,357] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:59,358] [INFO] Found 6/6 markers.
[2024-01-25 17:54:59,382] [INFO] Query marker FASTA was written to GCF_014384705.1_ASM1438470v1_genomic.fna/markers.fasta
[2024-01-25 17:54:59,382] [INFO] Task started: Blastn
[2024-01-25 17:54:59,382] [INFO] Running command: blastn -query GCF_014384705.1_ASM1438470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/reference_markers.fasta -out GCF_014384705.1_ASM1438470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:59,977] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:59,979] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:59,980] [INFO] Target genome list was writen to GCF_014384705.1_ASM1438470v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:00,097] [INFO] Task started: fastANI
[2024-01-25 17:55:00,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a8faa8-89ad-4d0e-b3d6-f7135825cfd7/GCF_014384705.1_ASM1438470v1_genomic.fna.gz --refList GCF_014384705.1_ASM1438470v1_genomic.fna/target_genomes.txt --output GCF_014384705.1_ASM1438470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:11,494] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:11,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:11,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:11,499] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:55:11,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:55:11,499] [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
Yeguia hominis	strain=NSJ-40	GCA_014384705.1	2763662	2763662	type	True	100.0	955	960	95	conclusive
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	81.7627	52	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:11,500] [INFO] DFAST Taxonomy check result was written to GCF_014384705.1_ASM1438470v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:11,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:11,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:11,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/checkm_data
[2024-01-25 17:55:11,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:11,531] [INFO] Task started: CheckM
[2024-01-25 17:55:11,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384705.1_ASM1438470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384705.1_ASM1438470v1_genomic.fna/checkm_input GCF_014384705.1_ASM1438470v1_genomic.fna/checkm_result
[2024-01-25 17:55:37,207] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:37,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:37,220] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:37,220] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:37,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384705.1_ASM1438470v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:37,220] [INFO] Task started: Blastn
[2024-01-25 17:55:37,220] [INFO] Running command: blastn -query GCF_014384705.1_ASM1438470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8038e393-52cd-4f62-96d2-7c48c2e1bca1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384705.1_ASM1438470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:38,327] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:38,330] [INFO] Selected 24 target genomes.
[2024-01-25 17:55:38,330] [INFO] Target genome list was writen to GCF_014384705.1_ASM1438470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:38,347] [INFO] Task started: fastANI
[2024-01-25 17:55:38,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a8faa8-89ad-4d0e-b3d6-f7135825cfd7/GCF_014384705.1_ASM1438470v1_genomic.fna.gz --refList GCF_014384705.1_ASM1438470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384705.1_ASM1438470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:47,541] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:47,544] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:47,545] [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
GCA_014384705.1	s__NSJ-40 sp014384705	100.0	955	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__NSJ-40	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002159845.1	s__Anaeromassilibacillus stercoravium	80.6333	56	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCA_018712265.1	s__Gallacutalibacter pullicola	76.6342	58	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Gallacutalibacter	95.0	98.09	98.02	0.89	0.86	4	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	76.2286	59	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:47,546] [INFO] GTDB search result was written to GCF_014384705.1_ASM1438470v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:47,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:47,548] [INFO] DFAST_QC result json was written to GCF_014384705.1_ASM1438470v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:47,549] [INFO] DFAST_QC completed!
[2024-01-25 17:55:47,549] [INFO] Total running time: 0h0m57s