Error on preprocess_features.py

[elliotnam]

Hi
when I run preprocess_features.py
I got out of index error from line 76

['>chr1']
Traceback (most recent call last):
File "./preprocess_features.py", line 420, in
main()
File "./preprocess_features.py", line 76, in main
chrom_lengths[a[0]] = int(a[1])
IndexError: list index out of range

so I printed a and the result is
['>chr1']

Is there anythin I missed
thx

[davek44]

Hi,

It appears that the program is examining a FASTA file where it expects a file containing a table with two columns. The first column should have the chromosome name, like "chr1". The second column should have the length of the chromosome. It's the "-c" option that specifies the path to this file. If you're not able to figure out why your command doesn't work, print it here, and I'll give you a hand.

Dave

[elliotnam]

Hi
I run this command

preprocess_features.py -y -m 200 -s 600 -o ../data/encode_roadmap -c
../data/genomes/hg19.fa ../data/sample_beds.txt

and i checked the file hg19.fa , on the first column, I found chr1 but
there is no length
like this

chr1
NNNNNNNNNNNNNNNNNNNNNNNN

Do I have wrong data file ?

2015-10-08 22:38 GMT+09:00 David Kelley [email protected]:

Hi,

It appears that the program is examining a FASTA file where it expects a
file containing a table with two columns. The first column should have the
chromosome name, like "chr1". The second column should have the length of
the chromosome. It's the "-c" option that specifies the path to this file.
If you're not able to figure out why your command doesn't work, print it
here, and I'll give you a hand.

Dave

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#1 (comment).

[davek44]

Yes, you'll want to provide the file human.hg19.genome in the directory data/genomes to the -c option.

[davek44]

Ah, I see that the tutorial specified the wrong file. I corrected the error.