Error: /lib64/libm.so.6: version `GLI BC_2.29' not found
SinhaI opened this issue · 0 comments
SinhaI commented
Hi, When I am running kb ref
command I am getting GLI BC_2.29
not found error message. Please see my command and the log contents below. I appreciate your help in this matter.
kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 intron_t2c.txt --workflow lamanno -n 4 hg19/inputs/GRCh37.primary_assembly.genome.fa hg19/inputs/gencode.primary_assembly.annotation.gtf
[2021-09-22 16:38:17,436] INFO [ref_lamanno] Concatenating cDNA and intron FASTAs to /crex/proj/snic2021-22-49/nobackup/Egle/RNA_velocity/scvelo/JMJ8/tmp/tmpq1p7cltf
[2021-09-22 16:38:53,325] INFO [ref_lamanno] Creating transcript-to-gene mapping at t2g.txt
[2021-09-22 16:39:38,863] INFO [ref_lamanno] Indexing cdna.fa to index.idx_cdna
[2021-09-22 16:39:39,981] ERROR [ref_lamanno] /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto)
/home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto)
/home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto)
/home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto)
/home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto)
[2021-09-22 16:39:39,982] ERROR [main] An exception occurred
Traceback (most recent call last):
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/main.py", line 1326, in main
COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/main.py", line 222, in parse_ref
ref_lamanno(
File "/home/indranil/.local/lib/python3.9/site-packages/ngs_tools/logging.py", line 62, in inner
return func(*args, **kwargs)
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/ref.py", line 748, in ref_lamanno
cdna_index_result = kallisto_index(
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/ref.py", line 239, in kallisto_index
run_executable(command)
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/dry/__init__.py", line 25, in inner
return func(*args, **kwargs)
File "/home/indranil/.local/lib/python3.9/site-packages/kb_python/utils.py", line 203, in run_executable
raise sp.CalledProcessError(p.returncode, ' '.join(command))
subprocess.CalledProcessError: Command '/home/indranil/.local/lib/python3.9/site-packages/kb_python/bins/linux/kallisto/kallisto index -i index.idx_cdna -k 31 cdna.fa' returned non-zero exit status 1.