I have this error in the submission, not sure how to solve it. This is part of the code: ``` def fill_feature_mat(rows): snps_featurs=pd.DataFrame(np.zeros([len(rows),len(my_snp_list)]),index=rows,columns=my_snp_list) for index in rows: vcf_file=validation_data.loc[index,'WES_mutationFileMutect'] if pd.isnull(vcf_file): continue vcf_file = vcf_dir + vcf_file f=pysam.VariantFile(vcf_file) for rec in f.fetch(): if (rec.id != None): if (rec.id in my_snp_list): snps_featurs.set_value(index,rec.id,1) return snps_featurs pool = Pool(ncpus) snps_featurs = pd.concat(pool.map(fill_feature_mat,sub_tasks)) pool.close() pool.join() ``` The error is: ``` Traceback (most recent call last): File "./prepare_data_matrix.py", line 160, in indel_variant_stat = pd.concat(pool.map(fill_caleb_features,sub_tasks)) File "/usr/lib/python2.7/multiprocessing/pool.py", line 251, in map return self.map_async(func, iterable, chunksize).get() File "/usr/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value NotImplementedError: seek not implemented in files compressed by method 1 ``` I don't have any error when I run it in my machine. Not sure why it can be run in docker. Really need some helps here. Thank you! Yichao

Created by yichao li unfashionable
pysam 0.9 fixed this problem.

HELP: pysam error? NotImplementedError page is loading…