Question: Tophat-fusion-post running errors
0
gravatar for Jackie
3.0 years ago by
Jackie70
United States
Jackie70 wrote:

Hi,

I am running tophat-fusion-post using this command line:

./tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 <path_to_bowtie_index>/<prefix>

The tophat-fusion output folder is in the same directory where I am running the command line.

and I got below error messages:

Traceback (most recent call last):

File "./tophat-fusion-post", line 2647, in <module> sys.exit(main())

File "./tophat-fusion-post", line 2615, in main map_fusion_kmer(bwt_idx_prefix, params, sample_updated)

File "./tophat-fusion-post", line 325, in map_fusion_kmer subprocess.call(cmd, stdout=open(output_dir + 'fusion_seq.bwtout', 'w'), stderr=open('/dev/null', 'w'))

File "/usr/lib64/python2.6/subprocess.py", line 478, in call p = Popen(popenargs, *kwargs)

File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__ errread, errwrite)

File "/usr/lib64/python2.6/subprocess.py", line 1238, in _execute_child raise child_exception

OSError: [Errno 2] No such file or directory

Can someone help debug this? Was anything missed here?

Thanks,

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Jackie70
0
gravatar for Jackie
3.0 years ago by
Jackie70
United States
Jackie70 wrote:

Hi,

Can anyone share some experience or provide some insights to this issue?

Thanks!

ADD COMMENTlink written 3.0 years ago by Jackie70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1094 users visited in the last hour