epinano_rms.py -> OverflowError: Python int too large to convert to C long

[DelphIONe]

Hi,

I tried using nanoRMS but got this result after a few hours :
python3 ~/softs/nanoRMS/epinano_RMS/epinano_rms.py -R ../Schizosaccharomyces_pombe.ASM294v2.dna.fa -b spliceRNA.bam -s sam2tsv.jar
Traceback (most recent call last):
/softs/nanoRMS/epinano_RMS/epinano_rms.py", line 341, in main
qual = np.array(qual.split(':')).astype(int)
OverflowError: Python int too large to convert to C long

In the output file, the end looks like this (outlier values):
tail spliceRNA.per.site.baseFreq.csv
I,4269446,T,-,1.0,41.000000,41.000000,0.000000,0.000000,1.000000,0.000000,0:0:0:1
I,4269447,C,-,1.0,20.000000,20.000000,0.000000,0.000000,1.000000,0.000000,0:1:0:0
I,4269448,A,-,1.0,15.000000,15.000000,0.000000,0.000000,0.000000,0.000000,1:0:0:0
I,4269449,T,-,1.0,15.000000,15.000000,0.000000,0.000000,0.000000,0.000000,0:0:0:1
I,4269450,T,-,1.0,19.000000,19.000000,0.000000,0.000000,0.000000,0.000000,0:0:0:1
I,4269451,T,-,1.0,38.000000,38.000000,0.000000,0.000000,0.000000,0.000000,0:0:0:1
I,4268964,T,+,16.0,7542127741.750000,9652977.000000,13052203563.568058,0.000000,0.062500,0.125000,0:0:0:14
I,4268965,A,+,15.0,16461672886.333334,17224824633.000000,13140429224.149954,0.066667,0.066667,0.200000,11:1:0:0
I,4268966,C,+,15.0,172349130788.000000,162844201138.000000,144758955815.042999,0.000000,0.000000,0.133333,0:13:0:0
I,4268967,T,+,15.0,1199212925532.666748,48264822741.000000,1661931610596.996582,0.000000,0.000000,0.066667,0:0:0:14

I suspect one error in freq files but why ?
grep "^I,4268964" spliceRNA.tmp_splitted_base_freq/small_*
spliceRNA.tmp_splitted_base_freq/small_36.freq:I,4268964,T,1,1,0,0,0,5:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_45.freq:I,4268964,T,1,1,0,0,0,20:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_47.freq:I,4268964,T,1,1,0,0,0,9:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_49.freq:I,4268964,T,1,0,0,0,1,0:,+,0:0:0:0::
spliceRNA.tmp_splitted_base_freq/small_54.freq:I,4268964,T,1,0,0,0,1,0:,+,0:0:0:0::
spliceRNA.tmp_splitted_base_freq/small_55.freq:I,4268964,T,1,1,0,0,0,37:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_56.freq:I,4268964,T,1,1,0,0,0,20:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_58.freq:I,4268964,T,2,2,0,0,0,3:30:,+,0:0:0:2:
spliceRNA.tmp_splitted_base_freq/small_59.freq:I,4268964,T,2,2,0,1,0,10:16:,+,0:0:0:2:
spliceRNA.tmp_splitted_base_freq/small_60.freq:I,4268964,T,1,1,0,0,0,49:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_63.freq:I,4268964,T,2,2,0,0,0,17:31:,+,0:0:0:2:
spliceRNA.tmp_splitted_base_freq/small_64.freq:I,4268964,T,1,1,0,0,0,14:,+,0:0:0:1:
spliceRNA.tmp_splitted_base_freq/small_68.freq:I,4268964,T,1,1,0,0,0,10:,+,0:0:0:1:

Perhaps, the problem is due to the presence of "::" (bold lines) at the end of some lines ?
Can you help me solve this problem ?

Thanks for your help,

[obegik]

Hi,

Have you tried running the script on a smaller window ? i.e. Perhaps you can only run it on a single chromosome?

[DelphIONe]

Hi,

Thanks for your reply!
I have tested by chromosome. On the chromosom I the problem is the same. The chromosome II it's ok ...
Splicing mapping can be a problem ?

[DelphIONe]

I add : for only one chromosom it's ok. For two others it's the same error "python overflow"
On one problematic chromosom, I've splitted the bam file in 2 and epinano_rms correctly finished. I cross finger for the last chromosom. For the next step, it's ok if I concatene all csv file ?