Traceback (most recent call last):


 "bcbio_nextgen_install.py", line 290, in <module>

main(parser.parse_args(), sys.argv[1:])


 "bcbio_nextgen_install.py", line 51, in main

subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args))


 "/usr/lib/python2.7/subprocess.py", line 190, in check_call

raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/mnt/e/bcbio/share/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/mnt/e/bcbio', '--genomes', 'hg38', '--aligners', 'bwa', '--aligners', 'bowtie2', '--data']' returned non-zero exit status 1

Traceback (most recent call last):


 "/home/kokyriakidis/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes

retrieve_fn(env, manager, gid, idx)


 "/home/kokyriakidis/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 519, in _prep_raw_index

get_index_fn(idx)(env, ref_file)


 "/home/kokyriakidis/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 678, in _index_bbmap

(cores, 3 * int(cores), dir_name, ref_file), shell=True)


 "/RED/BCBIO/RESOURCES/bcbio/anaconda/lib/python3.6/subprocess.py", line 311, in check_call

raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bbmap.sh -Xms1g -Xmx3g path=bbmap ref=/RED/BCBIO/RESOURCES/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa' returned non-zero exit status 1.
