tail: write error: Broken pipe

[GitHub-Lujianjun]

Hi，Olga. I got some error while running 3D-DNA pipeline as fellow: The runing command: run-asm-pipeline.sh --mode diploid draft.fasta merged_nodups.txt. The FINAL fasta is more fragmented than draft.fasta.

:( Some pairwise alignments are in conflict. Skipping merge block +utg5995_SmadenR5:::fragment_2 -utg1600_SmadenR5:::fragment_2 +utg1732_SmadenR5:::fragment_2 -utg82_SmadenR5:::fragment_2 +utg5995_SmadenR5:::fragment_4 +utg17_SmadenR5:::fragment_2 +utg1732_SmadenR5:::fragment_4 +utg82_SmadenR5:::fragment_2 +utg1600_SmadenR5:::fragment_4 -utg202_SmadenR5:::fragment_2 +utg1600_SmadenR5:::fragment_2 -utg1732_SmadenR5:::fragment_4 -utg5995_SmadenR5:::fragment_4 +utg202_SmadenR5:::fragment_2 -utg1600_SmadenR5:::fragment_4 -utg17_SmadenR5:::fragment_2! tail: write error: Broken pipe tail: write error ... ... ... ... ... Any ideas to figure out it? Many thanks! Lu

[ershuowang]

Hello, I met the same error when I ran the run-asm-pipeline.sh and I don't how to fix it.

Some of the error information: :| Warning: No input for label1 was provided. Default for label1 is ":::fragment_" :| Warning: No input for label2 was provided. Default for label2 is ":::debris" tail: error writing 'standard output': Broken pipe tail: error writing 'standard output': Broken pipe

[dudcha]

Hi Lu and ershuowang,

There are two typical reasons for the tail: write error. One is the bash version, it needs to be >=4 to support associative arrays, and another one is associated with SIGPIPE:

https://superuser.com/questions/554855/how-can-i-fix-a-broken-pipe-error

Since this is a common source of issue for people we'll be changing this bit of code to a more robust one, but it is not yet done as of right now.

(The other messages re "alignments are in conflict" and "no input label are provided" are warnings and have no baring on the result. Lu, please note that one wants to run diploid only if very certain that you need to deal with undercollapsed heterozygosity, and want to make sure you have everthing else in good shape before you move to merge.)

Hope this helps, Olga

[dudcha]

P.S.: see also this, more specifically re suggestion on sigpipe: https://github.com/theaidenlab/3d-dna/issues/29#issuecomment-437713884

[linshengnan2020]

hi, I got the same error , does this have an impact on the final result? Thank you very much!

[dudcha]

Hi,

If you are experiencing the same error than either you are using a review assembly file that is mismatched with the fasta, or you have issues with carriage return characters in either fasta or assembly file.

Best, Olga

On Oct 10, 2020, at 2:51 AM, linshengnan2020 [email protected] wrote:

 hi, I got the same error , does this have an impact on the final result? Thank you very much!

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[linshengnan2020]

sorry, I don't quite understand what you mean. Isn't the assembly file generated by the program and we just offer the fasta file.