[2024-01-24 13:09:34,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference
[2024-01-24 13:09:35,368] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,369] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg18b38882-d83d-470f-a972-e5c5c4d731c0/GCF_003688415.1_ASM368841v1_genomic.fna.gz | prodigal -d GCF_003688415.1_ASM368841v1_genomic.fna/cds.fna -a GCF_003688415.1_ASM368841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:41,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:41,905] [INFO] Task started: HMMsearch
[2024-01-24 13:09:41,905] [INFO] Running command: hmmsearch --tblout GCF_003688415.1_ASM368841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/reference_markers.hmm GCF_003688415.1_ASM368841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:42,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:42,173] [INFO] Found 6/6 markers.
[2024-01-24 13:09:42,202] [INFO] Query marker FASTA was written to GCF_003688415.1_ASM368841v1_genomic.fna/markers.fasta
[2024-01-24 13:09:42,208] [INFO] Task started: Blastn
[2024-01-24 13:09:42,208] [INFO] Running command: blastn -query GCF_003688415.1_ASM368841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/reference_markers.fasta -out GCF_003688415.1_ASM368841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:42,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:42,894] [INFO] Selected 26 target genomes.
[2024-01-24 13:09:42,894] [INFO] Target genome list was writen to GCF_003688415.1_ASM368841v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:42,954] [INFO] Task started: fastANI
[2024-01-24 13:09:42,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b38882-d83d-470f-a972-e5c5c4d731c0/GCF_003688415.1_ASM368841v1_genomic.fna.gz --refList GCF_003688415.1_ASM368841v1_genomic.fna/target_genomes.txt --output GCF_003688415.1_ASM368841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:59,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:59,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:59,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:59,532] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:59,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:59,532] [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
Umboniibacter marinipuniceus	strain=DSM 25080	GCA_003688415.1	569599	569599	type	True	100.0	889	890	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:09:59,534] [INFO] DFAST Taxonomy check result was written to GCF_003688415.1_ASM368841v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:59,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:59,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:59,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/checkm_data
[2024-01-24 13:09:59,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:59,562] [INFO] Task started: CheckM
[2024-01-24 13:09:59,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688415.1_ASM368841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688415.1_ASM368841v1_genomic.fna/checkm_input GCF_003688415.1_ASM368841v1_genomic.fna/checkm_result
[2024-01-24 13:10:23,930] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:23,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,948] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:23,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:23,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688415.1_ASM368841v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:23,949] [INFO] Task started: Blastn
[2024-01-24 13:10:23,949] [INFO] Running command: blastn -query GCF_003688415.1_ASM368841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c72d6b7-cf83-468f-b0cb-14cae9371daa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688415.1_ASM368841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:24,992] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:24,996] [INFO] Selected 28 target genomes.
[2024-01-24 13:10:24,996] [INFO] Target genome list was writen to GCF_003688415.1_ASM368841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:25,027] [INFO] Task started: fastANI
[2024-01-24 13:10:25,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b38882-d83d-470f-a972-e5c5c4d731c0/GCF_003688415.1_ASM368841v1_genomic.fna.gz --refList GCF_003688415.1_ASM368841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688415.1_ASM368841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:42,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:42,989] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:42,989] [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_003688415.1	s__Umboniibacter marinipuniceus	100.0	889	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-25080;g__Umboniibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013372965.1	s__Umboniibacter sp013372965	77.7053	62	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-25080;g__Umboniibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:42,991] [INFO] GTDB search result was written to GCF_003688415.1_ASM368841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:42,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:42,994] [INFO] DFAST_QC result json was written to GCF_003688415.1_ASM368841v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:42,994] [INFO] DFAST_QC completed!
[2024-01-24 13:10:42,994] [INFO] Total running time: 0h1m9s