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

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Issue #50 resolved
Stephan Christel created an issue

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

stephan@stephan-VirtualBox [~/Documents/pmi/hic-10mem-proto/chicago/designDir] >> : python ~/chicago/chicagoTools/
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

Reading rmap....
Traceback (most recent call last):
File "/home/stephan/chicago/chicagoTools/", line 134, in <module>
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:

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

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?



Comments (6)

  1. Mikhail Spivakov

    The input files to 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.

  2. Stephan Christel reporter

    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?

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