search

cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
GNU General Public License v3.0
45 stars 10 forks source link

raise Exception("Read %s has none or more than 2 clusters" % read) #13

Closed yuntwang closed 4 years ago

yuntwang commented 4 years ago

@cytham Hi，recent I use nanovar detect SV, the command line as follows: nanovar -x ont -t 10 -l 50 N01.bam sequences_new.fa N01 An error occurred after a while: nv_cov_upper.py:132: UserWarning: FixedFormatter should only be used together with FixedLocator ax.set_yticklabels(['{:,.1%}'.format(x) for x in vals]) Traceback (most recent call last): File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/bin/nanovar", line 479, in main() File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/bin/nanovar", line 307, in main run.cluster_extract() File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/lib/python3.7/site-packages/nanovar/nv_characterize.py", line 95, in cluster_extract self.contig, False, self.seed2) File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/lib/python3.7/site-packages/nanovar/nv_cluster.py", line 53, in sv_cluster mincov, File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/lib/python3.7/site-packages/nanovar/nv_cluster.py", line 166, in rangecollect classdict, ins_switch, mincov, infodict) File "/share/nas1/zhiyq/scripts/anaconda3/envs/nanovar/lib/python3.7/site-packages/nanovar/nv_cluster.py", line 270, in cluster raise Exception("Read %s has none or more than 2 clusters" % read) Exception: Read f1eb5b88-2771-4daa-bdbf-a9177b2e26a4~DBC65 has none or more than 2 clusters /opt/gridengine/default/spool/hpc02-c-0-141/job_scripts/7442838: line 1: 13810 Segmentation fault (core dumped)

How can I deal with it. Hope to get your reply.

cytham commented 4 years ago

Hi @yuntwang,

There seems to be an anomaly in the SV breakend clustering step. Do you mind running nanovar with the --debug option and send me the "subdata.tsv" and "parse1.tsv" files? The files might be too big to transfer over Github, thus you may want to share them over email or something else. My email is e0054302@u.nus.edu.

yuntwang commented 4 years ago

@cytham Sent mail, please check. thanks

cytham commented 4 years ago

@yuntwang Thanks for the files

I could not replicate the error using the files, they ran fine without raising any exception. The data is quite large and I realized you had the "Segmentation fault (core dumped)" error at the end which might indicate a memory issue. Your system might have run out of memory at the clustering step. I had roughly calculated that the clustering step for your data may take up about 15 GB of RAM. Can you try running again with a larger allocation of memory? Thanks

yuntwang commented 4 years ago

@cytham
ok, I try it.

cytham commented 4 years ago

@yuntwang managed to resolve the problem?

cytham commented 4 years ago

I assume the problem is resolved. Feel free to open this issue again.