ipyrad error step 6: ValueError: cannot copy sequence with size 298 to array axis with dimension 299

[IvonedeBem]

Hello,

I have been running ipyrad without any problem until now. However, I ran it for a new species and kept getting the error below:

[################### ] 99% 0:00:50 | building database
[####################] 100% 0:00:51 | building database
Encountered an Error.
Message: ValueError: cannot copy sequence with size 298 to array axis with dimension 299
Parallel connection closed.

All the other steps have worked ok, except that some of the samples present a really low number fro reads_consens

Full stats files

step 1: ./plate3_frostedgenomeREF085_fastqs/s1_demultiplex_stats.txt
step 2: ./plate3_frostedgenomeREF085_edits/s2_rawedit_stats.txt
step 3: ./plate3_frostedgenomeREF085_clust_0.85/s3_cluster_stats.txt
step 4: ./plate3_frostedgenomeREF085_clust_0.85/s4_joint_estimate.txt
step 5: ./plate3_frostedgenomeREF085_consens/s5_consens_stats.txt
step 6: None
step 7: None

Thanks for any suggestions and for your time!
Ivone

[isaacovercast]

Can you run step 6 again and include the '-d' flag to print debug info? Also can you show the ipyrad version with 'ipyrad -v'?

Also can you attach this file:
plate3_frostedgenomeREF085_consens/s5_consens_stats.txt

[IvonedeBem]

Thank you for the quick response. Here is the info:

version: ipyrad 0.9.53
s5 file: s5_consens_stats.txt
debug out file:
ipyrad_REF_out.txt

[isaacovercast]

That is a somewhat old version of ipyrad, can you update to the most recent version and try running step 6 again? We might have already solved this problem.

conda install -c conda-forge -c bioconda ipyrad=0.9.94

[IvonedeBem]

Thanks! I will ask the IT team from UF to install it. I will send news as soon as I get any.

Have a great day!