Pilfer Job killed.

[vivekruhela]

Hello,

I tried to get a piRNA cluster using your script pilfer.py. For a gzipped fastq file of size 573.0 Mb, I have got bam file from hg19 alignment using bowtie of size 2.9 Gb and bed file of size 9.2 Gb after subtracting it with ncRNA.bed. When I tried the following command
(python27) vivekr@sarabhai:~$ python /home/vivekr/PILFER/tools/pilfer.py -i /home/vivekr/piRNA/SRR7541164.bed > /home/vivekr/piRNA/SRR7541164.pirna_cluster

Killed

After very long pause, the job was killed. Does very heavy bed file responsible for this?

[vivekruhela]

Hi,

I would to add little update here. As I have mentioned earlier that job was killed probabely due to heavy baed file or less memory available [not sure]. So I tried with small bed file but I am still not getting any response. Here is the error:

(python27) vivekr@sarabhai:~$ head -n 100000 /home/vivekr/piRNA/SRR7541164.bed > /home/vivekr/piRNA/SRR7541164_1.bed ; python /home/vivekr/PILFER/tools/pilfer.py -i /home/vivekr/piRNA/SRR7541164_1.bed > /home/vivekr/piRNA/SRR7541164.pirna_cluster
/home/vivekr/PILFER/tools/pilfer.py:63: RuntimeWarning: invalid value encountered in double_scalars
if (row[4] - mean)/sd >= sd_factor:

Please suggest.

[LliliansCalvo]

Hi could you solve this ? I am encountering a similar problem.

[rishavray]

@LliliansCalvo This issue would mainly occur if your BED file is too large. The pipeline assumes that you have collapsed your BED file and the count is added up in field 5. What is the size of your BED file?

[Senimene]

Hello,
I'm encountering same problem :

/PILFER-master/tools/pilfer.py:63: RuntimeWarning: invalid value encountered
in double_scalars
if (row[4] - mean)/sd >= sd_factor:

The size of my bed file is ~1,63 Go
It contains 22556341 lines
and it looks linke this :
Contig923 62546 62570 HWI-ST225:358:C0BKDACXX:5:1205:12920:21054_1 255 +
Contig559 49825 49853 HWI-ST225:358:C0BKDACXX:5:1205:12956:21174_1 255 -
Contig282 108956 108983 HWI-ST225:358:C0BKDACXX:5:1205:13564:21023_1 255 +
Contig579 1774320 1774347 HWI-ST225:358:C0BKDACXX:5:1205:13614:21048_1 255 +
...

Could you help me please to resolve this problem ?
Thank you in advance

Best regards
IS

[rishavray]

Your BED file is not properly formatted for the pipeline. The reads need to be collapsed and the count should appear in column 5. Please use the scripts provided in the repo, that should help resolve the issue.

[Senimene]

Hi Rishav,
Noted.
I will correct the format
Thanks for your help :)
Best Regards
Imène