Closed tiagobrc closed 4 years ago
Hello, Thank you for your interest in BRAPeS! I added changes to BRAPeS that should fix this issue. Could you pull the new version and let me know if you still get this error?
Best, Shaked
Hi,
Thank you so much for your response!!
The problem disappeared indeed. But a new issue appeared.
It seems to be an issue with my glibc compiler. That's a tough one to solve in this server.
Thanks for your help!
2019-10-31 11:56:35.739137 Working on: ERR1467921
2019-10-31 11:56:35.770980 Pre-processing heavy chain
2019-10-31 11:56:35.793876 Did not find any V-J reads, searching for V-C and J-C reads:
Added 139 unmapped reads to the reads file
2019-10-31 11:56:45.921126 Pre-processing kappa chain
Added 957 unmapped reads to the reads file
2019-10-31 11:56:56.738079 Pre-processing lambda chain
2019-10-31 11:56:56.754041 Did not find any V-J reads, searching for V-C and J-C reads:
Added 222 unmapped reads to the reads file
2019-10-31 11:57:06.754495 Reconstructing heavy chains
/ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr)
2019-10-31 11:57:06.760834 Reconstructing kappa chains
/ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr)
2019-10-31 11:57:06.766358 Reconstructing lambda chains
/ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /ru-auth/local/home/trezende/localPrograms/BRAPeS//vdj.alignment.bcr)
2019-10-31 11:57:06.771920 Creating full BCR sequences
Traceback (most recent call last):
File "/ru-auth/local/home/trezende/localPrograms/BRAPeS/brapes.py", line 2157, in <module>
args.Fr)
File "/ru-auth/local/home/trezende/localPrograms/BRAPeS/brapes.py", line 52, in runBCRpipe
hvr_path, genome)
File "/ru-auth/local/home/trezende/localPrograms/BRAPeS/brapes.py", line 305, in runSingleCell
createTCRFullOutput(fastaDict, tcrF, fullTcrFileHeavy, bases, idNameDict, cSeq, cName, cId, oneSide)
File "/ru-auth/local/home/trezende/localPrograms/BRAPeS/brapes.py", line 1250, in createTCRFullOutput
tcrF = open(tcr, 'rU')
IOError: [Errno 2] No such file or directory: '/ru-auth/local/home/trezende/localPrograms/BRAPeS/Example/proc_data/ERR1467921/BRAPeS_out.reconstructed.junctions.heavy.fa'
Hi, thanks for this amazing software!.
I want to test the BCR reconstruction of BRAPeS but I am kind of stuck in the installation test. Could you please take a look at the output to see if something is wrong? I don't understand why this error is showing up.
Thanks