incomplete results

[sunshx-bioinfo]

Hi,

When i run RIsearch2 with multithreads, some gzip results are incomplete, i don't know why and how to resolve it. Here is my cmd:
RIsearch2 -q lncrna.fa -i mrna.suf -t 50 -s 10 -e -30 -l 20 -d 30 -z t04

[RTH-tools]

Hi,

to help you we would need a description of what you mean by incomplete and ideally a (minimal) example of input and output that demonstrates the problem. Also, which version of RIsearch2 and where did you obtain it?

Cheers, Christian.

[sunshx-bioinfo]

Hi,
Sorry for late reply.

I install RIsearch2 with conda: conda install rthtools::risearch,
and its version is v2.1 .

And I mean the result file, file with gzip format, is uncomplete, when i gunzip it, it throws me an error:
gunzip -c risearch_ENSG00000241743.out.gz >risearch_ENSG00000241743.out
Error:
gzip: risearch_ENSG00000241743.out.gz: unexpected end of file

I want to predict target genes of lncRNA, so i have about 20,000 mRNA sequences and 2,000 lncRNA sequences, and first i make
the index structure for the target sequences:
RIsearch2 -c mrna.fa -o mrna.suf -t 50
then predict target genes:
RIsearch2 -q lncrna.fa -i mrna.suf -t 50 -s 10 -e -30 -l 20 -d 30 -z t04

For each lncrna, RIsearh2 will give me one gzip result file, and most files are normal, but some are uncomplete, I will attach an uncomplete gzip result file.

I use qsub to submit this mission with 50 threads and 60 GB memory size. Maybe i need more memory ?

risearch_ENSG00000241743.out.gz

Best, sunshx

[RTH-tools]

I see. You have options that will heavily reduce the output, likely to the point of giving you no results

-e -30, try -e 0
-s 10, try -s 5
-d 30, try without it

This should give you some results with reasonable input. Likely more than you want but then you have something to start from when tightening the options.

Cheers, Christian.

[sunshx-bioinfo]

Hi, Christian,

Actually, my problem is that the gzip output is broken .

As you see, the attached file, risearch_ENSG00000241743.out.gz, is broken. You can gunzip it:
gunzip risearch_ENSG00000241743.out.gz -c > risearch_ENSG00000241743.out
the error, gzip: risearch_ENSG00000241743.out.gz: unexpected end of file, will be thrown, but risearch_ENSG00000241743.out is generated anyway. Let's see the last line:

it is uncomplete !
This is happend when I use RIsearch2 with multithreads and query fasta with multiple lncrnas, when i run with only ENSG00000241743 fasta sequence:
RIsearch2 -q ENSG00000241743.fa -i mrna.suf -t 2 -s 10 -e -30 -l 20 -d 30 -z t04, the generated risearch_ENSG00000241743.out.gz is normal.

[RTH-tools]

That sounds very odd. It is possible that there is something wrong with the input that makes risearch crash. Could you attach the input files as well.

Cheers, Christian.