Errors occured in SQuIRE Count step

[YayanFeng55]

Hi Yang,

I am so glad that you have developed such an amazing software for expression quantfication of transposable elements. But now it occured a weird error in Count step, the script I used worked well for other samples, but it reports error as follows now:

Warning: gene "TTTY3B" (on chrY) has reference transcripts on both strands? Traceback (most recent call last) : File "/home/fengy2/beegfs/Resources/miniconda3/envs/squire/bin/squire", line 11, in ‹module> load entry point ('SQuIRE' 'console scripts 'squire') () File "/mnt/beegfs/fengy2/Resources/miniconda3/sQuIRE/squire/cli.py",line156,inmain subargs. func (args subargs) File "/mnt/beegfs/fengy2/Resources/miniconda3/SQuIRE/squire/Count.py", line 1803, in main avg fraglength=uniquecount (unique bedfile, RepCalc dict.read locdict) File "/mnt/beegfs/fengy2/Resources/miniconda3/sQuIRE/squire/Count.py",line1229,inuniquecount unique_fragavg-unique fragsum/int (unique linecount) ZeroDivisionError: division by zero

How can I solve this problem? I have tried to use 80Gb larger memory to run Count. So I don't think it is not memory issues. Could you help me solve this problem? Thank you so much in advance.

Thanks, Yayan Feng

[CWYuan08]

Hi, @YayanFeng55, I have also encountered the same issue, have you fixed it so far? Thank you very much!

[jakewendt]

I had 4 out of my 13 samples doing this.

I added if unique_linecount > 0 else 0 to the end of line 1229.

sed -i 's/unique_fragavg=unique_fragsum\/int(unique_linecount)/unique_fragavg=unique_fragsum\/int\(unique_linecount\) if unique_linecount \> 0 else 0/' squire/Count.py

Worked for me. Well it didn't crash after that.