[2024-01-25 18:06:50,833] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:50,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:50,835] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference
[2024-01-25 18:06:51,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:51,989] [INFO] Task started: Prodigal
[2024-01-25 18:06:51,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b53b337-2817-4544-aff5-d3f8e0e37670/GCF_024498255.1_ASM2449825v1_genomic.fna.gz | prodigal -d GCF_024498255.1_ASM2449825v1_genomic.fna/cds.fna -a GCF_024498255.1_ASM2449825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:53,328] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:53,328] [INFO] Task started: HMMsearch
[2024-01-25 18:06:53,328] [INFO] Running command: hmmsearch --tblout GCF_024498255.1_ASM2449825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/reference_markers.hmm GCF_024498255.1_ASM2449825v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:53,499] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:53,500] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3b53b337-2817-4544-aff5-d3f8e0e37670/GCF_024498255.1_ASM2449825v1_genomic.fna.gz]
[2024-01-25 18:06:53,511] [INFO] Query marker FASTA was written to GCF_024498255.1_ASM2449825v1_genomic.fna/markers.fasta
[2024-01-25 18:06:53,511] [INFO] Task started: Blastn
[2024-01-25 18:06:53,511] [INFO] Running command: blastn -query GCF_024498255.1_ASM2449825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/reference_markers.fasta -out GCF_024498255.1_ASM2449825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:53,968] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:53,979] [INFO] Selected 14 target genomes.
[2024-01-25 18:06:53,979] [INFO] Target genome list was writen to GCF_024498255.1_ASM2449825v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:53,990] [INFO] Task started: fastANI
[2024-01-25 18:06:53,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b53b337-2817-4544-aff5-d3f8e0e37670/GCF_024498255.1_ASM2449825v1_genomic.fna.gz --refList GCF_024498255.1_ASM2449825v1_genomic.fna/target_genomes.txt --output GCF_024498255.1_ASM2449825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:57,488] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:57,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:57,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:57,493] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:57,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:57,494] [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
Mycoplasma elephantis	strain=ATCC 51980	GCA_000687815.1	114882	114882	type	True	78.4471	105	268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:57,495] [INFO] DFAST Taxonomy check result was written to GCF_024498255.1_ASM2449825v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:57,496] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:57,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:57,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/checkm_data
[2024-01-25 18:06:57,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:57,508] [INFO] Task started: CheckM
[2024-01-25 18:06:57,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498255.1_ASM2449825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498255.1_ASM2449825v1_genomic.fna/checkm_input GCF_024498255.1_ASM2449825v1_genomic.fna/checkm_result
[2024-01-25 18:07:08,666] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:08,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:08,682] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:08,682] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:08,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498255.1_ASM2449825v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:08,682] [INFO] Task started: Blastn
[2024-01-25 18:07:08,683] [INFO] Running command: blastn -query GCF_024498255.1_ASM2449825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1e9874d-592f-4460-ac42-5e220268f32f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498255.1_ASM2449825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:09,132] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:09,135] [INFO] Selected 14 target genomes.
[2024-01-25 18:07:09,135] [INFO] Target genome list was writen to GCF_024498255.1_ASM2449825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:09,153] [INFO] Task started: fastANI
[2024-01-25 18:07:09,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b53b337-2817-4544-aff5-d3f8e0e37670/GCF_024498255.1_ASM2449825v1_genomic.fna.gz --refList GCF_024498255.1_ASM2449825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498255.1_ASM2449825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:13,441] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:13,444] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:13,444] [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_900660595.1	s__Mycoplasma_H californicum_A	99.9791	268	268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000687815.1	s__Mycoplasma_H elephantis	78.4471	105	268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasma_H	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:13,445] [INFO] GTDB search result was written to GCF_024498255.1_ASM2449825v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:13,446] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:13,447] [INFO] DFAST_QC result json was written to GCF_024498255.1_ASM2449825v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:13,448] [INFO] DFAST_QC completed!
[2024-01-25 18:07:13,448] [INFO] Total running time: 0h0m23s