output files not as expected

elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

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output files not as expected #16

Open afadda91 opened 6 years ago

afadda91 commented 6 years ago

Hi, i'm getting the out put files all_clusters.pkl dbfile.sqlite, but not the table or gff3 or text files i'm supposed to get. There's no error and the run was smooth. what seems to be the issue? this is the command jitterbug.py --numCPUs 8 --bin_size 50000000 --output_prefix /HERVs/ /BAM_BWA/SRR2098232.sorted.bam hg19.te_annots.gff

thanks,

CPTPaso commented 3 years ago

I don't know if this is still relevant to you after more that 2 yrs but by chance I could solve your problem today. Just get into the outpput dir and use ls -la. Your output should be there as .TE_insertions_paired_clusters.gff3, however invisible if you ls -l and not ls -la.