samFilter: /lib64/libc.so.6: version `GLIBC_2.28' not found

[lkong888]

Hi, may I ask what's the dependency for samFilter? The following error shows when executing the samFilter file under bin directory. /lib64/libc.so.6: version GLIBC_2.28' not found (required by /users/ludwig/ebu571/ebu571/BIDseq/pseudoU-BIDseq-main/bin/samFilter) /lib64/libc.so.6: versionGLIBC_2.18' not found (required by /users/ludwig/ebu571/ebu571/BIDseq/pseudoU-BIDseq-main/bin/samFilter) /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /users/ludwig/ebu571/ebu571/BIDseq/pseudoU-BIDseq-main/bin/samFilter). Thanks.

[y9c]

Hi @lkong888, tis error is caused by the dependency of the gcc environment. You might use the legacy version of linux system. Coud you provide more details with the command you use and the version of your Linux?

[lkong888]

Hi @y9c , thank you so much for your reply. So, I downloaded the source code of this package, supplied it with the path of required packages(such as bowtie2, star), modified corresponding config file, and then ran the snakefile. Everything goes fine. But it turns out some executable file under the bin/ directory are binary and unable to be executed successfully(including samFilter and deletionFilter). Both show the same errors: /lib64/libc.so.6: version GLIBC_2.28' not found; /lib64/libc.so.6: versionGLIBC_2.18' not found and /lib64/libc.so.6: version `GLIBC_2.25' not found. I further checked and found that /lib64/libc.so.6 corresponds to libc-2.17.so. I think this might not be a good way to run your packages. But it would be great if samFilter and deletionFilter are readable files.

Another way to run your tool is "apptainer run docker://y9ch/bidseq", which is very neat. I'm running under "BIDseq" directory, which contains a fastq directory, a resource directory, bidseq_latest.sif and data.yaml. However, somehow it shows error saying that data.yaml can not be found! shouldn't data.yaml be at current working directory("BIDseq" in my case) according to the instructions?

I'd greatly appreciate it if you could help me with this problems. Thank you so much!

[y9c]

Yes. The environment is essential for running these tools, and this why I wrap everything in docker env to have better reproducibility. These tools are very simple, which are for prefilter putative deletion sites, and I made these tools in rust to prefiltering the data for speeding up. If you want to customized the pipeline from scratch, I do not recommend to add these step. You can call the deletion directly.

You do not need the "bidseq_latest.sif" file for runningm apptainer, since the command would pull the lastest verin automatically. I guess the reason you failed to parse the data.yaml file is your system setting. You might put your data in a mounted partion, and do not expose this directory to the apptainer correctly. Could you show the output of df command, and also the working direcotry (pwd).

[lkong888]

Thank you so much for your promt reply. the working sirectory is "/users/ludwig/ebu571/ebu571/BIDseq".(output from pwd) The output of df is: Filesystem 1K-blocks Used Available Use% Mounted on devtmpfs 197401632 0 197401632 0% /dev tmpfs 197414444 344 197414100 1% /dev/shm tmpfs 197414444 2066016 195348428 2% /run tmpfs 197414444 0 197414444 0% /sys/fs/cgroup /dev/mapper/system-root 41922560 11887632 30034928 29% / /dev/sda1 999320 244444 686064 27% /boot /dev/mapper/system-tmp 115880672 24202092 91678580 21% /tmp /dev/mapper/system-var 41922560 13709344 28213216 33% /var arc3-ib:/data/arc3a/PROCARDIS 41943040000 40298859520 1644180480 97% /arc/PROCARDIS arc4-ib:/data/arc4e/ckb 36700160000 19307322368 17392837632 53% /arc/ckb arc4-ib:/data/arc4e/jones 28311552000 27968046080 343505920 99% /arc/jones arc4-ib:/data/arc4e/zhang 130023424000 128974902272 1048521728 100% /arc/zhang arc4-ib:/data/arc4e/siebold 2097152000 1659095040 438056960 80% /arc/siebold arc4-ib:/srv/lamb 41922560 9348096 32574464 23% /arc/lamb arc4-ib:/data/arc4e/gilbert 33554432000 32849651712 704780288 98% /arc/gilbert bowmore-ib:/data/bowmore2 1093772779520 1087084765184 6688014336 100% /data/bowmore2 bowmore-ib:/data/bowmore 488293539840 427964615680 60328924160 88% /data/bowmore 10.128.0.11@tcp,10.128.0.12@tcp:10.128.0.13@tcp,10.128.0.14@tcp:10.128.0.15@tcp,10.128.0.16@tcp:10.128.0.17@tcp,10.128.0.18@tcp:/exafs 4875413354112 2201522321108 2428854818668 48% /exafs1 WTGPFS3 8304319266816 6264249810944 2040069455872 76% /gpfs3 WTGPFS2 3835196080128 3310553634816 524642445312 87% /gpfs2 tmpfs 39482892 0 39482892 0% /run/user/37786 tmpfs 39482892 0 39482892 0% /run/user/37756 tmpfs 39482892 0 39482892 0% /run/user/31010 tmpfs 39482892 0 39482892 0% /run/user/38275 tmpfs 39482892 0 39482892 0% /run/user/38616 tmpfs 39482892 0 39482892 0% /run/user/37936 tmpfs 39482892 0 39482892 0% /run/user/37628 tmpfs 39482892 0 39482892 0% /run/user/37014 tmpfs 39482892 0 39482892 0% /run/user/38544 tmpfs 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[y9c]

I am not sure if /users/ludwig directory is a soft link or not based on the provided information. But you can try adding --bind /users/ludwig/ebu571 or --bind /users into the command right after 'run'.

[y9c]

How about try realpath data.yaml for more details

[lkong888]

Hi,

Both "apptainer run --bind /users/ludwig/ebu571 docker://y9ch/bidseq " and "apptainer run --bind /users docker://y9ch/bidseq" do not work. For more detailed information, current path: /users/ludwig/ebu571/ebu571/BIDseq (pwd) realpath: /gpfs3/well/ludwig/users/ebu571/BIDseq (realpath /users/ludwig/ebu571/ebu571/BIDseq) realpath of data.yaml: /gpfs3/well/ludwig/users/ebu571/BIDseq/data.yaml (realpath data.yaml).

Thanks.

[y9c]

Yes. This is the bug we have mentioned in the previous thread. /gpfs3 is not exposed to appraiser.

Try --bind /gpfs3

[lkong888]

apptainer run --bind /gpfs3 docker://y9ch/bidseq does not work. The same error keeps showing even when I replace --bind /gpfs3 with /gpfs3/well or /gpfs3/well/ludwig or /gpfs3/well/ludwig/users or /gpfs3/well/ludwig/users/ebu571. I also tried to give the realpath of data.yaml (apptainer run docker://y9ch/bidseq -c /gpfs3/well/ludwig/users/ebu571/BIDseq/data.yaml), but it still does not work.

[y9c]

Thank you for the update. Some time Apptainer to not have the privilege to parse some path due to permission setting. I guess you are running the code on HPC without root privilege. You might need to ask the manager to set up apptainer properly.

[y9c]

Hi Kong, if possible we can have another attempt to run the code. Based on your input, I guess your server have a complex directory structure. --bind /gpfs3/well/ludwig/users:/users/ludwig/ebu571 might works

[lkong888]

Hi,

That's great. With " --bind /gpfs3/well/ludwig/users:/users/ludwig/ebu571 ", apptainer can find the data.yaml successfully. But it shows the following errors: Traceback (most recent call last): File "/pipeline/micromamba/lib/python3.10/site-packages/snakemake/init.py", line 564, in snakemake workflow = Workflow( File "/pipeline/micromamba/lib/python3.10/site-packages/snakemake/workflow.py", line 242, in init self.sourcecache = SourceCache() File "/pipeline/micromamba/lib/python3.10/site-packages/snakemake/sourcecache.py", line 336, in init os.makedirs(self.cache, exist_ok=True) File "/pipeline/micromamba/lib/python3.10/os.py", line 215, in makedirs makedirs(head, exist_ok=exist_ok) File "/pipeline/micromamba/lib/python3.10/os.py", line 215, in makedirs makedirs(head, exist_ok=exist_ok) File "/pipeline/micromamba/lib/python3.10/os.py", line 215, in makedirs makedirs(head, exist_ok=exist_ok) File "/pipeline/micromamba/lib/python3.10/os.py", line 225, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/users/ludwig/ebu571/.cache'

I think the cmd tries to make a directory under '/users/ludwig/ebu571/.cache', but the permission is denied. I guess I may need to consult the manager tomorrow.

Thank you so much for the troubleshooting. it's very helpful.

[y9c]

Great to know. The permission management of this sever is a little bit complicated. You can try --bind /gpfs3/well/ludwig/users/ebu571/BIDseq:/users/ludwig/ebu571/ebu571/BIDseq, before contacting the system manager

[lkong888]

Yes, the directory structure system is quite complicated. With "apptainer run --bind /gpfs3/well/ludwig/users/ebu571/BIDseq:/users/ludwig/ebu571/ebu571/BIDseq docker://y9ch/bidseq", it fails to find the data.yaml again.

Is it possible to specify a place(eg, /gpfs3/well/ludwig/users/ebu571) instead of "/users/ludwig/ebu571" to make the directory?

[y9c]

Hi, @lkong888. Thank you very much for posting the error log for debug. I believe that now the problem is on the Linux server side. I would like to close this issue first and you can report or share your findings in new issue.