symbol lookup error

[tracychew]

symbol lookup error

[dlandsman]

We’ll get back to you next week. The person working on this is on vacation at the moment. David ===================================== David Landsman, Ph.D. Chief, Computational Biology Branch NCBI, NLM, NIH Bethesda, Maryland, U.S.A. ===================================== I will be teleworking between the hours of 9am and 5pm but I might surprise you with a reply outside of those hours. From: tracyc ***@***.***> Sent: Wednesday, April 14, 2021 12:38 AM To: ncbi/TPMCalculator ***@***.***> Cc: Subscribed ***@***.***> Subject: [ncbi/TPMCalculator] symbol lookup error (#69) Hi, I installed TPMcalculator using conda. I have aligned FASTQs to GRCh38 with bowtie and have obtained GTF from Ensembl. I am not too sure what to make of this error - any help would be great, thanks. Tracy ***@***.*** Scripts]$ /scratch/er01/apps/miniconda3/bin/TPMCalculator -g ../References/GRCh38_v103/Homo_sapiens.GRCh38.103.gtf -b ../RNA_cutadapt_min17_align_Coenen-Stass/HB10-aln-hg38.sorted.dedup.bam Reading GTF file ... Done in 163.879 seconds Parsing sample: HB10-aln-hg38.sorted.dedup/scratch/er01/apps/miniconda3/bin/TPMCalculator: symbol lookup error: /scratch/er01/apps/miniconda3/bin/TPMCalculator: undefined symbol: _ZN8BamTools11SamSequenceC1ERKS0_ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#69>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADLJW6YN2YEELKL3Z4XQIEDTIUL3ZANCNFSM424S4EAA>.

[r78v10a07]

The error you're seeing is related to the BAMTools dynamic libraries used by TPMCalculator.
My guess is that you have a different BAMTools version installed in someplace and reachable via the LD_LIBRARY_PATH env variable.

Could you try this before running TPMCalculator?

export LD_LIBRARY_PATH=/scratch/er01/apps/miniconda3/lib/

[tracychew]

Hi, thanks for getting back to me! I'm still getting the same error:

[tc6463@gadi-login-07 Scripts]$ export LD_LIBRARY_PATH=/scratch/er01/apps/miniconda3/lib/
[tc6463@gadi-login-07 Scripts]$ echo $LD_LIBRARY_PATH
/scratch/er01/apps/miniconda3/lib/
[tc6463@gadi-login-07 Scripts]$ /scratch/er01/apps/miniconda3/bin/TPMCalculator -g ../References/GRCh38_v103/Homo_sapiens.GRCh38.103.gtf -b ../RNA_cutadapt_min17_align_Coenen-Stass/HB10-aln-hg38.sorted.dedup.bam
Reading GTF file ...
Done in 158.582 seconds
Parsing sample: HB10-aln-hg38.sorted.dedup/scratch/er01/apps/miniconda3/bin/TPMCalculator: symbol lookup error: /scratch/er01/apps/miniconda3/bin/TPMCalculator: undefined symbol: _ZN8BamTools11SamSequenceC1ERKS0_

[r78v10a07]

Hi,
Could you try to find the location of the libbamtools.so file?
You could try:

find /scratch/er01/apps/miniconda3/ -name libbamtools.so

[tracychew]

Hi, looks like I do have it in a couple locations including, I tried setting LB_LIBRARY_PATH to either location but I still get the same error:

[tc6463@gadi-login-06 Scripts]$ find /scratch/er01/apps/miniconda3/ -name libbamtools.so
/scratch/er01/apps/miniconda3/pkgs/bamtools-2.5.1-h9a82719_8/lib/libbamtools.so
find: '/scratch/er01/apps/miniconda3/pkgs/urllib3-1.25.8-py37_0fgotlour': Permission denied
find: '/scratch/er01/apps/miniconda3/pkgs/urllib3-1.25.8-py37_077kc6tii': Permission denied
find: '/scratch/er01/apps/miniconda3/pkgs/libgcc-ng-9.1.0-hdf63c60_0zi7updp_': Permission denied
find: '/scratch/er01/apps/miniconda3/pkgs/xz-5.2.4-h14c3975_45xw96xfv': Permission denied
/scratch/er01/apps/miniconda3/lib/libbamtools.so
[tc6463@gadi-login-06 Scripts]$ export LD_LIBRARY_PATH=/scratch/er01/apps/miniconda3/lib/
[tc6463@gadi-login-06 Scripts]$ /scratch/er01/apps/miniconda3/bin/TPMCalculator -g ../References/GRCh38_v103/Homo_sapiens.GRCh38.103.gtf -b ../RNA_cutadapt_min17_align_Coenen-Stass/HB10-aln-hg38.sorted.dedup.bam
Reading GTF file ...
Done in 162.429 seconds
Parsing sample: HB10-aln-hg38.sorted.dedup/scratch/er01/apps/miniconda3/bin/TPMCalculator: symbol lookup error: /scratch/er01/apps/miniconda3/bin/TPMCalculator: undefined symbol: _ZN8BamTools11SamSequenceC1ERKS0_
[tc6463@gadi-login-06 Scripts]$ export LD_LIBRARY_PATH=^C
[tc6463@gadi-login-06 Scripts]$ export LD_LIBRARY_PATH=/scratch/er01/apps/miniconda3/pkgs/bamtools-2.5.1-h9a82719_8/lib                                  [tc6463@gadi-login-06 Scripts]$ /scratch/er01/apps/miniconda3/bin/TPMCalculator -g ../References/GRCh38_v103/Homo_sapiens.GRCh38.103.gtf -b ../RNA_cutadapt_min17_align_Coenen-Stass/HB10-aln-hg38.sorted.dedup.bam
Reading GTF file ...
Done in 161.304 seconds
Parsing sample: HB10-aln-hg38.sorted.dedup/scratch/er01/apps/miniconda3/bin/TPMCalculator: symbol lookup error: /scratch/er01/apps/miniconda3/bin/TPMCalculator: undefined symbol: _ZN8BamTools11SamSequenceC1ERKS0_

[r78v10a07]

For some reason that I don't know TPMCalculator is not using the BAMtools library.
I would recommend to compile TPMCalculator.

First compile and install BAMTools:

https://github.com/ncbi/TPMCalculator#bamtools

Then, clone the source code:

git clone https://github.com/ncbi/TPMCalculator

and run make

[tracychew]

I tried that in the past, I tried it again and figured out the issue now that I know bamtools was the problem, thanks!

I had to git clone TPMCalculator in the directory where BAMTools was compiled and installed (instead of a separate directory - how we would normally structure tool installs)

[tc6463@gadi-login-03 TPMCalculator]$ make
"make" -f nbproject/Makefile-Release.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory '/scratch/er01/apps/TPMCalculator'
"make"  -f nbproject/Makefile-Release.mk bin/TPMCalculator
make[2]: Entering directory '/scratch/er01/apps/TPMCalculator'
mkdir -p build/Release/GNU-MacOSX/src
rm -f "build/Release/GNU-MacOSX/src/DiffExpIR.o.d"
g++ -g   -c -O2 -Iincludes -I../../bamtools/include/bamtools -std=c++14 -MMD -MP -MF "build/Release/GNU-MacOSX/src/DiffExpIR.o.d" -o build/Release/GNU-MacOSX/src/DiffExpIR.o src/DiffExpIR.cpp
src/DiffExpIR.cpp:26:10: fatal error: api/BamReader.h: No such file or directory
 #include "api/BamReader.h"
          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [nbproject/Makefile-Release.mk:94: build/Release/GNU-MacOSX/src/DiffExpIR.o] Error 1
make[2]: Leaving directory '/scratch/er01/apps/TPMCalculator'
make[1]: *** [nbproject/Makefile-Release.mk:85: .build-conf] Error 2
make[1]: Leaving directory '/scratch/er01/apps/TPMCalculator'
make: *** [nbproject/Makefile-impl.mk:40: .build-impl] Error 2

[r78v10a07]

Is this solved?

[tracychew]

Yes, thank you :)