tail: write error: Broken pipe

[hope tis]

Dear,

I get follows error output when used the 3D DNA for my genome:

My command:

run-asm-pipeline.sh -m diploid -i 10000 -r 2 -q 5 genome.fasta merged_nodups.txt

And error output:

tail: write error

tail: write error

tail: write error: Broken pipe

Because the run-asm-pipeline.sh is a wrapper script and I don't know which script caused this error.

Thanks

Zhongping Xu

[Olga Dudchenko]

Hello Zhongping,

I am afraid I cannot say much from just the messages you are listing. I would suggest checking the dependencies: a typical problem is old GNU utils. Also, note that diploid version of the pipeline is currently under development and will be updated within the next few weeks. If you are certain you need to run the diploid version of 3D-DNA I would suggest running the original commit from March 2017 rather than the latest updates that focus on $1K mammalian genomes.

Best,
Olga

[shengnan lin]

HI，

I also encountered this error, I checked my GNU utils and they are meet the requirements:

GNU Awk 4.0.2
sort (GNU coreutils) 8.22
GNU Parallel 2018
GNU bash, version 4.2.46(2)-release

My command:

bash /home/linshengnan/01_software/3d-dna/run-asm-pipeline.sh -m haploid -i 15000 $PWD/references/$ref $PWD/aligned/merged_nodups.mnd &> 3d.log

 error output:

tail: write error: Broken pipe
tail: write error: Broken pipe
tail: write error
tail: write error: Broken pipe
tail: write error: Broken pipe
tail: write error
tail: write error: Broken pipe
tail: write error: Broken pipe
tail: write error: Broken pipe

could you give me some advise ? Thank you very much!

在 2018年3月31日星期六 UTC+8下午9:23:45，hope tis写道：

[Olga Dudchenko]

Hello Shengnan,

Check for carriage return characters in fasta. See other threads on the forum for relevant sed command if needed.

Best,

Olga