ERROR in rule align about aeron

[SchulzLab]

Hi Br1anChou,
how did you create the .gfa file? Which gtf did you use for it?

Bests,
Marcel

[maickrau]

Hi Br1anChou,

Could you please post the log files "tmp/aligner_stdout_ReferenceTranscriptFastaFile_HumanUpdated38V5.txt" and "tmp/aligner_stderr_ReferenceTranscriptFastaFile_HumanUpdated38V5.txt"?

[Br1anChou]

Hi Marcel,
I used AeronScripts/GraphBuilder.py to create the .gfa file, and downloaded the .gtf file and genome sequence file from ensembl.org. when I run Graph building step, everything looks good. Please NOTE, the line 69 of ParseGTF.py, incorrect used of tabs and spaces, this will couse some errors, but I have corrected it.
Thanks again, I would appreciate it if you can provide some necessary test files and corresponding results, to help me determine which step go wrong.

Best,
Brian

[Br1anChou]

Hi maickrau,
I checked tmp/aligner_stderr_ReferenceTranscriptFastaFile_HumanUpdated38V5.txt, the version of libstdc++.so.6 is too low, I fixed it. Thanks for your suggestions, the software has not reported errors now.

[SchulzLab]

Hi Brian,
I am happy that it works now. Thanks for spotting the error in the ParseGTF.py file. We have fixed it.
Cheers,
Marcel