[2024-01-24 13:41:10,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference
[2024-01-24 13:41:11,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,764] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,764] [INFO] Running command: gunzip -c /var/lib/cwl/stgc930a8aa-deaa-43fc-90ab-c2916130d68c/GCF_009696145.1_ASM969614v1_genomic.fna.gz | prodigal -d GCF_009696145.1_ASM969614v1_genomic.fna/cds.fna -a GCF_009696145.1_ASM969614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:17,728] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:17,728] [INFO] Task started: HMMsearch
[2024-01-24 13:41:17,728] [INFO] Running command: hmmsearch --tblout GCF_009696145.1_ASM969614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/reference_markers.hmm GCF_009696145.1_ASM969614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:17,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:17,956] [INFO] Found 6/6 markers.
[2024-01-24 13:41:17,981] [INFO] Query marker FASTA was written to GCF_009696145.1_ASM969614v1_genomic.fna/markers.fasta
[2024-01-24 13:41:17,981] [INFO] Task started: Blastn
[2024-01-24 13:41:17,981] [INFO] Running command: blastn -query GCF_009696145.1_ASM969614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/reference_markers.fasta -out GCF_009696145.1_ASM969614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:18,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:18,583] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:18,583] [INFO] Target genome list was writen to GCF_009696145.1_ASM969614v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:18,599] [INFO] Task started: fastANI
[2024-01-24 13:41:18,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgc930a8aa-deaa-43fc-90ab-c2916130d68c/GCF_009696145.1_ASM969614v1_genomic.fna.gz --refList GCF_009696145.1_ASM969614v1_genomic.fna/target_genomes.txt --output GCF_009696145.1_ASM969614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,998] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:33,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,998] [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
Pseudoramibacter porci	strain=RF-744-FAT-4	GCA_009696145.1	2606631	2606631	type	True	100.0	682	684	95	conclusive
Pseudoramibacter alactolyticus	strain=ATCC 23263	GCA_000185505.1	113287	113287	type	True	77.2447	104	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,002] [INFO] DFAST Taxonomy check result was written to GCF_009696145.1_ASM969614v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:34,002] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:34,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:34,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/checkm_data
[2024-01-24 13:41:34,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:34,032] [INFO] Task started: CheckM
[2024-01-24 13:41:34,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696145.1_ASM969614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696145.1_ASM969614v1_genomic.fna/checkm_input GCF_009696145.1_ASM969614v1_genomic.fna/checkm_result
[2024-01-24 13:41:58,471] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,488] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696145.1_ASM969614v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,489] [INFO] Task started: Blastn
[2024-01-24 13:41:58,489] [INFO] Running command: blastn -query GCF_009696145.1_ASM969614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5a0c01-fac6-41b6-8dea-dfbbbd3c47c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696145.1_ASM969614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,360] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:59,361] [INFO] Target genome list was writen to GCF_009696145.1_ASM969614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:59,413] [INFO] Task started: fastANI
[2024-01-24 13:41:59,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgc930a8aa-deaa-43fc-90ab-c2916130d68c/GCF_009696145.1_ASM969614v1_genomic.fna.gz --refList GCF_009696145.1_ASM969614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696145.1_ASM969614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:07,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,770] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:07,770] [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_009696145.1	s__Pseudoramibacter porci	100.0	682	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Pseudoramibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002396065.1	s__Pseudoramibacter fermentans	86.4856	332	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Pseudoramibacter	95.0	96.84	95.63	0.89	0.79	5	-
GCF_000185505.1	s__Pseudoramibacter alactolyticus	77.2447	104	684	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Pseudoramibacter	95.0	97.37	97.37	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,772] [INFO] GTDB search result was written to GCF_009696145.1_ASM969614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:07,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:07,775] [INFO] DFAST_QC result json was written to GCF_009696145.1_ASM969614v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:07,775] [INFO] DFAST_QC completed!
[2024-01-24 13:42:07,775] [INFO] Total running time: 0h0m57s