Run SampComp error

[q1134269149]

Hi, I ran the SampComp for my data with the command line "nanocompore sampcomp --sample_yaml At_mtb_wt.yaml --fasta $transRef --min_coverage 5 -t 25 --outpath At_mtb_col0_nanocompore.out --overwrite --outprefix mtbcol0 --comparison_methods GMM,KS,TT,MW --logit", however, I got an error in the log as follow: _"(base) [shihan@covid nanocompore]$ tail nanopolish_fip37.log File "/home/shihan/anaconda3/envs/nanopolish/lib/python3.6/multiprocessing/queues.py", line 240, in _feed send_bytes(obj) File "/home/shihan/anaconda3/envs/nanopolish/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes self._send_bytes(m[offset:offset + size]) File "/home/shihan/anaconda3/envs/nanopolish/lib/python3.6/multiprocessing/connection.py", line 393, in _sendbytes header = struct.pack("!i", n) struct.error: 'i' format requires -2147483648 <= number <= 2147483647 100%|█████████▉| 5516/5518 [4:47:31<00:06, 3.13s/ Processed References] Loading SampCompDB Calculate results "

How did this error happen? Does it affect my subsequent analysis? And Do I need to run again? Thanks hqin

[a-slide]

Hi hqin, Looks like you hit the limit of integers size supported on your system. This is another edge case we have never seen yet. I suspect it might be due to a transcript with a very high coverage. Could you try to rerun sampcomp with option --downsample_high_coverage 5000 ? If you still have an error can you please attach the full log output ? Thanks

[q1134269149]

Hi, I ran nanocompore SampComp with command line: "nanocompore sampcomp --sample_yaml At_mtb_wt_2.yaml --fasta Araport11_genes.201606.cdna.fasta --mincoverage 5 -t 10 --outpath nanocompore.out --overwrite --outprefix At --comparison_methods GMM,KS --logit --downsample_high_coverage 2000", However, I met a problem. When the process reach to 60%, a child thread of the program became the zombie state and didn't continue the output, although the command line shows the running. At first I thought I didn't add the parameter of "--downsample_highcoverage 2000", but I re-strart with this parameter, it also got the same situation. The log file were the following: " nohup: ignoring input Initialising SampComp and checking options Initialising Whitelist and checking options Reading eventalign index files References found in index: 32966 Filtering out references with low coverage References remaining after reference coverage filtering: 4757 Starting data processing 60%|██████ | 2859/4757 [3:06:32<2:03:50, 3.91s/ Processed References] "_ I do not know how to solve this problem, I wonder if you have any better suggestions. Thanks hqin

[tleonardi]

Hi, it seems this is related to #163. Could you try running Nanocompore again using the version just released (1.0.1)? If it still get stuck please port the log file generated.

[tleonardi]

closing due to inactivity