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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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SNAP failed #190

Closed jwidmann closed 8 years ago

jwidmann commented 8 years ago

Hi, i get the following Error when running transrate on my assembly:

[ERROR] 2016-04-01 16:08:24 : Snap failed
Welcome to SNAP version 1.0beta.18.

mmap failed.
MemMapDataReader: fail to map Tissue5_right.fastq at 0,10388449043
SNAP exited with exit code 1 from line 2233 of file SNAPLib/DataReader.cpp

Is this simply because I have too much input reads for SNAP to map, or is this something else? This is the command I used:

transrate --assembly Trinity_allTissues.fasta --left Tissue1_left.fastq,Tissue2_left.fastq,Tissue3_left.fastq,Tissue4_left.fastq,Tissue5_left.fastq --right Tissue1_right.fastq,Tissue2_right.fastq,Tissue3_right.fastq,Tissue4_right.fastq,Tissue5_right.fastq --threads 8 --output /Transrate

Any suggestions? Best wishes

blahah commented 8 years ago

SNAP should be able to handle any number of input reads - more likely this is a bug. I am currently working through some SNAP bugs to see if I can pin down what causes them and ask the SNAP developers to fix them.

Have you tried running the same command again? The bug may be non-deterministic, in which case it might work the second time round.

jwidmann commented 8 years ago

Yep, tried twice the same command, resulting in the same Error. But maybe the third time is the charm, i'll give it another try. Thanks for your fast reply :)

blahah commented 8 years ago

I'm currently working on the next release of transrate which includes various fixes to SNAP - can you try it and see if it solves your problem? Download links below

blahah commented 8 years ago

Ah, and please make sure to delete the output directory from the earlier runs, or give the new run a different output location.

jwidmann commented 8 years ago

Hmm, the next release gives the same error (but line 2283). Mapping only this specific read set works fine.

blahah commented 8 years ago

hi @jwidmann, the latest release of transrate v1.0.3 now includes the latest version of SNAP and Salmon as well as some other bug fixes. Please update and try your analysis again. Hopefully this will solve the problem - if not please re-open the issue. Many thanks for your patience :)

Jinjie-Duan commented 7 years ago

Hi, @blahah ,I installed the latest version of transrate v 1.0.3. But I still got the same followoing message about SNAP failed. Would you please help on it? Thanks!

[ERROR] 2017-02-23 16:07:32 : Snap failed Welcome to SNAP version 1.0dev.96.

mmap failed. MemMapDataReader: fail to map /home/jjduan/python/01highQualityData/withoutN-trimlastbase/110902_SN132_B_L002_R2_GLQ-13b.fastq at 0,1966390515 SNAP exited with exit code 1 from line 2283 of file SNAPLib/DataReader.cpp