cc.plot.png, cc.fraglen, no such file or directory
shirleytemples opened this issue · 5 comments
When I run the command
"caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda",
it returns that
"error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
STDOUT=
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c38f96bf-ffcf-4f31-b063-3f901c0137ad/call-xcor/shard-1/attempt-2/execution/.cc.plot.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c38f96bf-ffcf-4f31-b063-3f901c0137ad/call-xcor/shard-1/attempt-2/execution/.cc.fraglen.txt': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c38f96bf-ffcf-4f31-b063-3f901c0137ad/call-xcor/shard-1/attempt-2/execution/.cc.plot.pdf': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c38f96bf-ffcf-4f31-b063-3f901c0137ad/call-xcor/shard-1/attempt-2/execution/.cc.qc': No such file or directory
2022-01-24 00:55:43,410|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1"
I am not too sure how to eliminate this error and get the json file to run.
Did you install pipeline's Conda environment (scripts/install_conda_env.sh)?
What is your pipeline and caper versions? Both should be >= 2.0.0.
Please run this for debugging:
$ source activate encode-chip-seq-pipeline-spp
# find conda env's bin/ and lib/ directory
(encode-chip-seq-pipeline-spp) $ which bedtools
/users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/bedtools
# check if libreadline* exists
(encode-chip-seq-pipeline-spp) $ ls -l /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline*
-rw-rw-r-- 7 leepc12 users 568982 Aug 28 2018 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.a
lrwxrwxrwx 1 leepc12 users 18 Dec 7 13:11 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so -> libreadline.so.7.0
lrwxrwxrwx 1 leepc12 users 18 Dec 7 13:11 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so.7 -> libreadline.so.7.0
-rwxrwxr-x 7 leepc12 users 372072 Aug 28 2018 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so.7.0Yup, I installed pipeline's Conda environment and my version for conda is 4.10.3 and for caper is 2.1.2.
I ran the debugging steps that you mentioned.
find conda env's bin/ and lib/ directory
$ source activate encode-chip-seq-pipeline-spp
(encode-chip-seq-pipeline-spp) $ which bedtools
/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/bedtools
check if libreadline* exists
(encode-chip-seq-pipeline-spp) shirleytemples@DESKTOP-9R1GDM5:~/chip-seq-pipeline2$ ls -l /home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline*
-rw-rw-r-- 4 shirleytemples shirleytemples 568982 Aug 28 2018 /home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.a
lrwxrwxrwx 1 shirleytemples shirleytemples 18 Jan 23 23:44 /home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so -> libreadline.so.7.0
lrwxrwxrwx 1 shirleytemples shirleytemples 18 Jan 23 23:44 /home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so.7 -> libreadline.so.7.0
-rwxrwxr-x 4 shirleytemples shirleytemples 372072 Aug 28 2018 /home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libreadline.so.7.0
####The outputs seem to match what you have. However, when I try again and rerun the command
caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda
it returns the same error
STDERR=/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
STDOUT=
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/902d009e-1aa9-45c7-acb9-0fb3a04e6527/call-xcor/shard-1/attempt-2/execution/*.cc.plot.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/902d009e-1aa9-45c7-acb9-0fb3a04e6527/call-xcor/shard-1/attempt-2/execution/*.cc.fraglen.txt': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/902d009e-1aa9-45c7-acb9-0fb3a04e6527/call-xcor/shard-1/attempt-2/execution/*.cc.plot.pdf': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/902d009e-1aa9-45c7-acb9-0fb3a04e6527/call-xcor/shard-1/attempt-2/execution/*.cc.qc': No such file or directory
2022-01-24 16:46:26,383|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2022-01-24 16:46:26,384|caper.cli|ERROR| Check stdout in `/home/shirleytemples/chip-seq-pipeline2/cromwell.out.3
Not too sure how to further debug the issue.
Just wanted to follow up and see if there are any additional steps I could do, I am still stuck on this. Any help would be much appreciated! @leepc12
This looks like Conda's issue (missing readline 6 for old R versions).
It's currently very hard to resolve conflicts without conda-forge.
I will fix this in the next release. Until then please manually install readline 6.0 on your system.
For example (Debian-based OS)
$ sudo apt-get install libreadline6Thanks for your help, it works now. I had to do several other things for it to work as libreadline6 is no longer available.
sudo apt-get install libreadline-dev
cd /lib/x86_64-linux-gnu/
sudo ln -s libreadline.so.8.0 libreadline.so.6
sudo apt-get install libncurses5