Problems assembling reads with Trinity

usegalaxy.org support
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#1

Greetings everyone.
I am new using Galaxy. I have raw data of 3 conditions, paired-ended, 2 biological replicates. The readings are from mRNA from hemocytes of a mollusc called Argopecten purpuratus. I perform assembling using Trinity and send this error:

2020/08/18 12:55:19.07 parrot_run[42627] child:43170 notice: warning: system call 237 (mbind) not supported for program /cvmfs/main.galaxyproject.org/venv/bin/python3.6

Please tell me if there is a memory problem or there is problem running the program.
Whatever the problem, can you propose the following steps? i’ll be very thankful.

I am waiting for your responses.

Best regards,

Felipe Stambuk.

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#2

These messages are warnings - did you end up with a red (error) dataset in your history? If so, can you use the “bug” icon on that dataset to send us an error report?

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#3

@nate i have reported the error with the bug icon. My question was another.
Thanks to trying to help anyway.

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#4

Hi @FELIPE_STAMBUK_OPAZO

If you are still having problems…

  1. The reads are RNA-seq, correct? That is what Trinity is expecting as an input.

  2. Did you check and run QA on your reads before assembly? This is an important step not to miss. (example tools: FastQC > Trimmomatic > FastQC > MultiQC)

  3. Are the datasets very large? If so, you may need to downsample to reduce the size. Do this after QA. (example: Seqtk tool group has a few choices)

  4. If you cannot solve the problem, would you please send in the bug report again? Include a link to this Q&A in the comments section so we can link the report to your question here.

Thanks!