help for tail: Error writing 'Standard Output ': Broken pipe

[freefly jin]

Hi,
Thank you for your useful pipeline. Recently, I was using the software of 3d-dna and met the problem like "tail: Error writing 'Standard Output ': Broken pipe " in finalize step. I saw your suggestions and solved the problem by trying dd insertion into lines 62 and 64 of 3d-dna/finalize/construct-fasta-from-asm.sh(https://github.com/aidenlab/3d-dna/issues/29), however, I don't know where to add dd or other solutions. I also read similar problems from others in https://groups.google.com/g/3d-genomics, and there seems to be no clear. Could you help me solve this problem that has been bothering me for a long time? Looking forward to your reply. Thank you very much! 

[Olga Dudchenko]

hi,

Before changing anything, make sure you are using the right files for review. The most common reason for this is not the OS issue, but rather people using the wrong assembly file. Another possible issue are special characters at the end of the sequence identifiers in the fasta.

Thanks,

Olga