samFilter: /lib64/libc.so.6: version `GLIBC_2.28' not found about pseudou-bidseq

[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: version GLIBC_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 39482892 0 39482892 0% /run/user/38676
tmpfs 39482892 0 39482892 0% /run/user/38486
tmpfs 39482892 0 39482892 0% /run/user/34807
tmpfs 39482892 0 39482892 0% /run/user/38252
tmpfs 39482892 0 39482892 0% /run/user/38805
tmpfs 39482892 0 39482892 0% /run/user/34713
tmpfs 39482892 0 39482892 0% /run/user/38554
tmpfs 39482892 0 39482892 0% /run/user/38318
tmpfs 39482892 0 39482892 0% /run/user/34881
tmpfs 39482892 0 39482892 0% /run/user/38587
tmpfs 39482892 0 39482892 0% /run/user/38342
tmpfs 39482892 0 39482892 0% /run/user/38635
tmpfs 39482892 0 39482892 0% /run/user/37959
tmpfs 39482892 0 39482892 0% /run/user/38334
tmpfs 39482892 0 39482892 0% /run/user/38199
tmpfs 39482892 0 39482892 0% /run/user/37925
tmpfs 39482892 0 39482892 0% /run/user/38296
tmpfs 39482892 4 39482888 1% /run/user/34854
tmpfs 39482892 0 39482892 0% /run/user/38274
tmpfs 39482892 0 39482892 0% /run/user/4406
tmpfs 39482892 0 39482892 0% /run/user/38291
tmpfs 39482892 0 39482892 0% /run/user/37871
tmpfs 39482892 0 39482892 0% /run/user/34817
tmpfs 39482892 0 39482892 0% /run/user/37336
tmpfs 39482892 0 39482892 0% /run/user/38048
tmpfs 39482892 0 39482892 0% /run/user/38798
tmpfs 39482892 0 39482892 0% /run/user/2947
tmpfs 39482892 0 39482892 0% /run/user/34858
tmpfs 39482892 0 39482892 0% /run/user/4142
tmpfs 39482892 0 39482892 0% /run/user/4332
tmpfs 39482892 0 39482892 0% /run/user/38715
tmpfs 39482892 0 39482892 0% /run/user/37604
tmpfs 39482892 0 39482892 0% /run/user/38455
tmpfs 39482892 0 39482892 0% /run/user/38808
tmpfs 39482892 0 39482892 0% /run/user/38392
tmpfs 39482892 0 39482892 0% /run/user/3967
tmpfs 39482892 0 39482892 0% /run/user/37099
tmpfs 39482892 0 39482892 0% /run/user/38648
tmpfs 39482892 0 39482892 0% /run/user/37884
tmpfs 39482892 0 39482892 0% /run/user/34705
tmpfs 39482892 0 39482892 0% /run/user/37155
tmpfs 39482892 0 39482892 0% /run/user/4284
tmpfs 39482892 0 39482892 0% /run/user/34828
tmpfs 39482892 0 39482892 0% /run/user/37919
tmpfs 39482892 0 39482892 0% /run/user/37121
tmpfs 39482892 0 39482892 0% /run/user/37286
tmpfs 39482892 0 39482892 0% /run/user/30111
tmpfs 39482892 0 39482892 0% /run/user/38359
tmpfs 39482892 0 39482892 0% /run/user/38248
tmpfs 39482892 0 39482892 0% /run/user/37957
tmpfs 39482892 0 39482892 0% /run/user/34926
tmpfs 39482892 0 39482892 0% /run/user/38786
tmpfs 39482892 0 39482892 0% /run/user/30132
tmpfs 39482892 0 39482892 0% /run/user/37796
tmpfs 39482892 0 39482892 0% /run/user/37726
tmpfs 39482892 0 39482892 0% /run/user/38557
tmpfs 39482892 0 39482892 0% /run/user/34872
tmpfs 39482892 0 39482892 0% /run/user/34884
tmpfs 39482892 0 39482892 0% /run/user/38131
tmpfs 39482892 0 39482892 0% /run/user/34799
tmpfs 39482892 0 39482892 0% /run/user/37106
tmpfs 39482892 0 39482892 0% /run/user/34853
tmpfs 39482892 0 39482892 0% /run/user/37264
tmpfs 39482892 0 39482892 0% /run/user/4233
tmpfs 39482892 0 39482892 0% /run/user/38473
tmpfs 39482892 0 39482892 0% /run/user/2658
tmpfs 39482892 0 39482892 0% /run/user/34932
tmpfs 39482892 0 39482892 0% /run/user/38567
tmpfs 39482892 0 39482892 0% /run/user/4417
tmpfs 39482892 0 39482892 0% /run/user/37406
tmpfs 39482892 0 39482892 0% /run/user/37215
tmpfs 39482892 0 39482892 0% /run/user/38568
tmpfs 39482892 0 39482892 0% /run/user/37981
tmpfs 39482892 0 39482892 0% /run/user/38360
tmpfs 39482892 0 39482892 0% /run/user/37315
tmpfs 39482892 0 39482892 0% /run/user/38128
tmpfs 39482892 0 39482892 0% /run/user/2503
tmpfs 39482892 0 39482892 0% /run/user/38788
tmpfs 39482892 0 39482892 0% /run/user/38477
tmpfs 39482892 0 39482892 0% /run/user/37295
tmpfs 39482892 0 39482892 0% /run/user/38804
tmpfs 39482892 0 39482892 0% /run/user/38332
tmpfs 39482892 0 39482892 0% /run/user/3032
tmpfs 39482892 0 39482892 0% /run/user/38556
tmpfs 39482892 0 39482892 0% /run/user/38215
tmpfs 39482892 0 39482892 0% /run/user/38659
tmpfs 39482892 0 39482892 0% /run/user/37053
tmpfs 39482892 0 39482892 0% /run/user/3891
tmpfs 39482892 0 39482892 0% /run/user/38658
tmpfs 39482892 0 39482892 0% /run/user/37686
tmpfs 39482892 0 39482892 0% /run/user/38633
tmpfs 39482892 0 39482892 0% /run/user/34694
tmpfs 39482892 0 39482892 0% /run/user/38570
tmpfs 39482892 0 39482892 0% /run/user/34857
tmpfs 39482892 0 39482892 0% /run/user/4244
tmpfs 39482892 0 39482892 0% /run/user/38224
tmpfs 39482892 0 39482892 0% /run/user/37876
tmpfs 39482892 0 39482892 0% /run/user/37942
tmpfs 39482892 0 39482892 0% /run/user/38750
tmpfs 39482892 0 39482892 0% /run/user/38251
tmpfs 39482892 0 39482892 0% /run/user/38097
tmpfs 39482892 0 39482892 0% /run/user/38772
tmpfs 39482892 0 39482892 0% /run/user/38611
tmpfs 39482892 0 39482892 0% /run/user/38784
tmpfs 39482892 0 39482892 0% /run/user/37352
tmpfs 39482892 0 39482892 0% /run/user/37044
tmpfs 39482892 0 39482892 0% /run/user/3232
tmpfs 39482892 0 39482892 0% /run/user/38509
tmpfs 39482892 0 39482892 0% /run/user/37970
tmpfs 39482892 0 39482892 0% /run/user/38072
tmpfs 39482892 0 39482892 0% /run/user/37090
tmpfs 39482892 0 39482892 0% /run/user/30046
tmpfs 39482892 0 39482892 0% /run/user/38613
tmpfs 39482892 0 39482892 0% /run/user/34718
tmpfs 39482892 0 39482892 0% /run/user/37469
tmpfs 39482892 0 39482892 0% /run/user/38503
tmpfs 39482892 0 39482892 0% /run/user/37951
tmpfs 39482892 0 39482892 0% /run/user/38304
tmpfs 39482892 0 39482892 0% /run/user/38722
tmpfs 39482892 0 39482892 0% /run/user/38576
tmpfs 39482892 0 39482892 0% /run/user/38137
tmpfs 39482892 0 39482892 0% /run/user/38652
tmpfs 39482892 0 39482892 0% /run/user/34700
tmpfs 39482892 0 39482892 0% /run/user/37290
tmpfs 39482892 0 39482892 0% /run/user/38336
tmpfs 39482892 0 39482892 0% /run/user/38601
tmpfs 39482892 0 39482892 0% /run/user/37288
tmpfs 39482892 0 39482892 0% /run/user/37887
tmpfs 39482892 0 39482892 0% /run/user/38406
tmpfs 39482892 0 39482892 0% /run/user/30094
tmpfs 39482892 0 39482892 0% /run/user/38584
tmpfs 39482892 0 39482892 0% /run/user/38589
tmpfs 39482892 0 39482892 0% /run/user/38448
tmpfs 39482892 0 39482892 0% /run/user/34905
tmpfs 39482892 0 39482892 0% /run/user/3623
tmpfs 39482892 0 39482892 0% /run/user/38262
tmpfs 39482892 0 39482892 0% /run/user/38161
tmpfs 39482892 0 39482892 0% /run/user/38095
tmpfs 39482892 0 39482892 0% /run/user/37510
tmpfs 39482892 0 39482892 0% /run/user/34906
tmpfs 39482892 0 39482892 0% /run/user/38707
tmpfs 39482892 0 39482892 0% /run/user/37094
tmpfs 39482892 0 39482892 0% /run/user/38169
tmpfs 39482892 0 39482892 0% /run/user/38302
tmpfs 39482892 0 39482892 0% /run/user/37869

[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.