makeDesignFiles.py: ValueError: invalid literal for int() with base 10: 'start'

[Stephan Christel]

Hi there!

Since a couple days I am working on getting a capture HiC analysis working, and now I stumpled across the following error when calling makeDesignFiles.py

stephan@stephan-VirtualBox [~/Documents/pmi/hic-10mem-proto/chicago/designDir] >> : python ~/chicago/chicagoTools/makeDesignFiles.py
Located baitmapfile pb10_rp4_baited_fragments.baitmap in .
Located rmapfile 10mem_pb10_rp4_proto.rmap in .
Using options:
minFragLen=150, maxFragLen=40000, maxLBrownEst=1500000, binsize=20000, removeb2b=True, removeAdjacent=True
rmapfile=./10mem_pb10_rp4_proto.rmap
baitmapfile=./pb10_rp4_baited_fragments.baitmap
outfilePrefix=./10mem_pb10_rp4_proto

Reading rmap....
Traceback (most recent call last):
File "/home/stephan/chicago/chicagoTools/makeDesignFiles.py", line 134, in <module>
st.append(int(l[1]))
ValueError: invalid literal for int() with base 10: 'start'

‌

I created the rmap and baitmap files via R, basically using the digest file of HiCup as a template. The files look like this:

head(*.rmap)
chr start end fragmentID
NZ_AJWE01000001.1 1 12 Frag_000001
NZ_AJWE01000001.1 13 54 Frag_000002
NZ_AJWE01000001.1 55 66 Frag_000003
NZ_AJWE01000001.1 67 279 Frag_000004
NZ_AJWE01000001.1 280 380 Frag_000005
NZ_AJWE01000001.1 381 489 Frag_000006
NZ_AJWE01000001.1 490 1240 Frag_000007
NZ_AJWE01000001.1 1241 1270 Frag_000008
NZ_AJWE01000001.1 1271 1282 Frag_000009
NZ_AJWE01000001.1 1283 1324 Frag_000010

head(*.baitmap)
chr start end fragmentID baitAnnotation
RP4 1 60 Frag_617455 RP4_1
RP4 61 219 Frag_617456 RP4_61
RP4 220 243 Frag_617457 RP4_220
RP4 244 424 Frag_617458 RP4_244
RP4 425 443 Frag_617459 RP4_425
RP4 444 554 Frag_617460 RP4_444
RP4 555 705 Frag_617461 RP4_555
RP4 706 750 Frag_617462 RP4_706
RP4 751 782 Frag_617463 RP4_751
RP4 783 830 Frag_617464 RP4_783

‌

Does anybody see something wrong with them, and can explain what I need to do to fix this issue?

Thanks!

‌

/stephan

[Mikhail Spivakov]

The input files to makeDesignFiles.py should have no header, which is exactly what the script is complaining about.

By the way, if you are using a different enzyme to HindIII (and in particular, a four-cutter), you may want to reduce the minFragLen parameter setting, both here and for the Chicago R package.

[Stephan Christel]

Hi, thanks for the quick reply.

I already assumed that it might be the headers, but when I removed those, the error message instead complained about Frag_000001.

Is there no text allowed in the fragmentID either?

[Mikhail Spivakov]

Correct, ids should be numeric as well.