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hakyim / TO-DELETE-PrediXcan

Code for the in-dev PrediXcan Project
MIT License
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getting error while running PrediXcan.py for Predicting/Imputing Expression #11

Closed tushardave26 closed 8 years ago

tushardave26 commented 8 years ago

Hello Authors,

I am facing an error while I am running PrediXcan.py script for Predicting/Imputing Expression. Below is my command line:

python ./PrediXcan.py --predict --dosages dosages --dosages_prefix chr --sample dosages/sample.txt -- weights Liver_LASSO.db --output_dir .

Below are first 3 lines of my sample.txt file: 10878 10878 0 0 0 0 -9 11655 11655 0 0 0 0 -9 12201 12201 0 0 0 0 -9

Below is the log file content:

2016-04-14 14:06:55.609509 Preloading weights... 2016-04-14 14:06:56.201847 Processing chr1.dosage.data.txt.gz 2016-04-14 14:24:10.396559 Processing chr10.dosage.data.txt.gz 2016-04-14 14:35:32.422774 Processing chr11.dosage.data.txt.gz 2016-04-14 14:46:11.936055 Processing chr12.dosage.data.txt.gz 2016-04-14 14:56:42.306676 Processing chr13.dosage.data.txt.gz 2016-04-14 15:04:40.451957 Processing chr14.dosage.data.txt.gz 2016-04-14 15:12:00.289541 Processing chr15.dosage.data.txt.gz 2016-04-14 15:18:19.583822 Processing chr16.dosage.data.txt.gz 2016-04-14 15:25:31.726997 Processing chr17.dosage.data.txt.gz 2016-04-14 15:31:46.137181 Processing chr18.dosage.data.txt.gz 2016-04-14 15:38:07.463976 Processing chr19.dosage.data.txt.gz 2016-04-14 15:43:57.293840 Processing chr2.dosage.data.txt.gz 2016-04-14 16:01:55.391602 Processing chr20.dosage.data.txt.gz 2016-04-14 16:07:00.779805 Processing chr21.dosage.data.txt.gz 2016-04-14 16:10:12.819881 Processing chr22.dosage.data.txt.gz 2016-04-14 16:13:29.788277 Processing chr3.dosage.data.txt.gz 2016-04-14 16:28:40.400313 Processing chr4.dosage.data.txt.gz 2016-04-14 16:44:31.586482 Processing chr5.dosage.data.txt.gz 2016-04-14 16:58:26.106604 Processing chr6.dosage.data.txt.gz 2016-04-14 17:12:43.945125 Processing chr7.dosage.data.txt.gz 2016-04-14 17:25:40.343552 Processing chr8.dosage.data.txt.gz 2016-04-14 17:38:02.067445 Processing chr9.dosage.data.txt.gz Traceback (most recent call last): File "/data/ssalimi/packages/PrediXcan/Software/PrediXcan.py", line 198, in main() File "/data/ssalimi/packages/PrediXcan/Software/PrediXcan.py", line 181, in main transcription_matrix.save(PRED_EXP_FILE) File "/data/ssalimi/packages/PrediXcan/Software/PrediXcan.py", line 118, in save outfile.write('\t'.join(next(sample_generator)) + '\t' + '\t'.join(map(str, self.D[:,col]))+'\n') StopIteration

I am not sure why I am having this error. Can you please help me to understand the issue and also help me to resolve it?

Thanks.

Best, Tushar

ScottPDickinson commented 8 years ago

Hi Tushar,

We'll be closing this thread since we're addressing this in another location. Also, we have an update to the repository that makes this error less cryptic. You can find it at hakyimlab/PrediXcan.

Best, Scott