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