Output Files - status and *.txt
Opened this issue · 5 comments
Hi!
I have tested your tool on four different bam files. All the runs finished with an empty *.txt files and with no status output file. what is that means?
Thank you
Hi @danablanc, are you receiving any error messages?
@rbonneville
No, I got the following prints:
--difference-threshold 0.4
--distance-threshold 0.187
--dissimilarity-threshold 0.07
Calculating instability scores ...
done.
MANTIS complete.
Could you please post your command line for running MANTIS?
python mantis.py --bedfile /home/mantis_loci_6.bed --genome /home/refgenome.fa -n /Disk_D/normal_sorted.bam -t /home/bamForMsi/1.bam -o /Disk_D/mantis_results/1.txt --threads 12 -mrr 7
As mentioned, there was no status output file, and the .txt had only the name of the columns (Locus Normal_Reads Tumor_Reads Difference Distance Dissimilarity) with no values in it. Also, I have noticed that the filtered file had no values in it, only the columns names.
Maybe your tumor or nomal file doesn't match the filter standard, so the result is empty.
Please ensure that:
Minimum average read quality >=25,
Minimum average locus quality>= 30,
Minimum (unclipped/unmasked) read length>=35