Insertion detection

[Madelinehazel]

Hello,

When I try to run enhanced insertion detection, I get an error message. This is my command:

run_metasv.py --reference /mnt/data/GRCh37_bcgsc/GRCh37-lite.fa --boost_sc --sample A48018 --bam /mnt/data/A48018_2_lanes_dupsFlagged.bam --spades /home/hpcuser01/SPAdes-3.6.2-Linux/spades.py --age /home/hpcuser01/AGE/age_align --num_threads 50 --workdir A48018_work_boostins --outdir A48018_out_boostinst --max_ins_intervals 500000 --isize_mean 462 --isize_sd 119 --chromosomes X

And the error message:

ERROR 2016-06-24 11:59:42,265 run_spades_single-<Process(PoolWorker-51, started daemon)> Caught exception in worker thread
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/metasv/run_spades.py", line 75, in run_spades_single
retcode = cmd.run(cmd_log_fd_out=spades_log_fd, timeout=timeout)
File "/usr/local/lib/python2.7/dist-packages/metasv/external_cmd.py", line 20, in run
self.p = subprocess.Popen(self.cmd, stderr=cmd_log_fd_err, stdout=cmd_log_fd_out)
File "/usr/lib/python2.7/subprocess.py", line 710, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

What might be the issue here?

Also, the http://bioinform.github.io/metasv/ website should be updated for enhancing insertion detection (.e.g boost_ins is no longer an option).

Thanks for your help,
Madeline

[Chandralinjo]

Hi,

I know this thread is a year old now, but I have the same issue right now. Do you remember how did you (if you did) fix it?

Thanks,
Boris

[Chandralinjo]

Turns out I was missing a '/' in my path to spades.py, it was evading me for a day and a half. So, if anyone else is having the same problem, triplecheck your paths!

Good luck!

[marghoob]

Thanks, I am glad it worked for you!