[2024-01-24 12:53:41,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference
[2024-01-24 12:53:43,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,049] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,049] [INFO] Running command: gunzip -c /var/lib/cwl/stg105d359c-d434-434d-a36d-04f731fde353/GCF_024338845.1_ASM2433884v1_genomic.fna.gz | prodigal -d GCF_024338845.1_ASM2433884v1_genomic.fna/cds.fna -a GCF_024338845.1_ASM2433884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:44,548] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:44,548] [INFO] Task started: HMMsearch
[2024-01-24 12:53:44,548] [INFO] Running command: hmmsearch --tblout GCF_024338845.1_ASM2433884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/reference_markers.hmm GCF_024338845.1_ASM2433884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:44,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:44,919] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg105d359c-d434-434d-a36d-04f731fde353/GCF_024338845.1_ASM2433884v1_genomic.fna.gz]
[2024-01-24 12:53:44,933] [INFO] Query marker FASTA was written to GCF_024338845.1_ASM2433884v1_genomic.fna/markers.fasta
[2024-01-24 12:53:44,933] [INFO] Task started: Blastn
[2024-01-24 12:53:44,933] [INFO] Running command: blastn -query GCF_024338845.1_ASM2433884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/reference_markers.fasta -out GCF_024338845.1_ASM2433884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,906] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,910] [INFO] Selected 13 target genomes.
[2024-01-24 12:53:47,912] [INFO] Target genome list was writen to GCF_024338845.1_ASM2433884v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:47,920] [INFO] Task started: fastANI
[2024-01-24 12:53:47,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg105d359c-d434-434d-a36d-04f731fde353/GCF_024338845.1_ASM2433884v1_genomic.fna.gz --refList GCF_024338845.1_ASM2433884v1_genomic.fna/target_genomes.txt --output GCF_024338845.1_ASM2433884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:52,511] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:52,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:52,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:52,550] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:52,550] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:52,551] [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 imitans	strain=ATCC 51306	GCA_000518305.1	29560	29560	type	True	80.468	172	327	95	below_threshold
Mycoplasmoides gallisepticum	strain=NCTC10115	GCA_900476085.1	2096	2096	type	True	79.8687	156	327	95	below_threshold
Mycoplasmoides gallisepticum	strain=ATCC 19610	GCA_000428645.1	2096	2096	type	True	79.6723	155	327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:52,552] [INFO] DFAST Taxonomy check result was written to GCF_024338845.1_ASM2433884v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:52,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:52,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:52,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/checkm_data
[2024-01-24 12:53:52,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:52,580] [INFO] Task started: CheckM
[2024-01-24 12:53:52,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024338845.1_ASM2433884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024338845.1_ASM2433884v1_genomic.fna/checkm_input GCF_024338845.1_ASM2433884v1_genomic.fna/checkm_result
[2024-01-24 12:54:09,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:09,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:09,552] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:09,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:09,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024338845.1_ASM2433884v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:09,554] [INFO] Task started: Blastn
[2024-01-24 12:54:09,554] [INFO] Running command: blastn -query GCF_024338845.1_ASM2433884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83444c93-252d-41cb-a5e1-d777f072d86a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024338845.1_ASM2433884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:10,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:10,073] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:10,073] [INFO] Target genome list was writen to GCF_024338845.1_ASM2433884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:10,109] [INFO] Task started: fastANI
[2024-01-24 12:54:10,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg105d359c-d434-434d-a36d-04f731fde353/GCF_024338845.1_ASM2433884v1_genomic.fna.gz --refList GCF_024338845.1_ASM2433884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024338845.1_ASM2433884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:13,201] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:13,216] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:54:13,216] [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_000518305.1	s__Mycoplasmoides imitans	80.4048	171	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014068355.1	s__Mycoplasmoides tullyi	79.8886	160	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476085.1	s__Mycoplasmoides gallisepticum	79.8687	156	327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	98.49	97.87	0.96	0.93	28	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:13,218] [INFO] GTDB search result was written to GCF_024338845.1_ASM2433884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:13,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:13,223] [INFO] DFAST_QC result json was written to GCF_024338845.1_ASM2433884v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:13,223] [INFO] DFAST_QC completed!
[2024-01-24 12:54:13,223] [INFO] Total running time: 0h0m32s