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STOmics / SAW

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Why can't I just use docker mount to run the command? #78

Closed RADIOMUMM closed 1 month ago

RADIOMUMM commented 7 months ago

I ran the reference genome construction of SAW with the following command:

docker run -P -v /data/storeData/ztron/Project/STOmics_test/ref/:/database stomics/saw:07.0.0 mapping -h

Then error ‘standard_init_linux.go:190: exec user process caused "exec format error" ’

Why can't you run it directly? My server version is configured as follows：

LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.4.1708 (Core) Release: 7.4.1708 Codename: Core

TheSallyGardens commented 7 months ago

Hi,we recommend using docker version 20.10.8 or higher.

RADIOMUMM commented 5 months ago

Hi,we recommend using docker version 20.10.8 or higher.

Hi I ended up choosing singularity and built the SIF file with the following command. singularity build --tmpdir . /tmp . /SAW_7.0.sif docker-archive:///data/storeData/ztron/Project/STOmics_test/img/stomics_saw_07_0_0.tar In the meantime my docker has been upgraded to the latest version（24.0.7）

However, the error still occurs when you finally use the following command singularity exec "/data/storeData/ztron/Project/STOmics_test/SAW_7.0.sif" mapping --help The error is as follows: /opt/saw_v7.0.0_software/pipeline/mapping/bcSTAR: error while loading shared libraries: libnuma.so.1: cannot open shared object file: No such file or directory

Can you help me? Thank you very much. best!

TheSallyGardens commented 1 month ago

@RADIOMUMM Hi, you can be updated to SAW v7.0.1 to resolve it. Best wish!

myshu2017-03-14 commented 1 month ago

@RADIOMUMM Hi, you can be updated to SAW v7.0.1 to resolve it. Best wish!

Hi, I updated to SAW v7.0.1. But the error is still there.

/opt/saw_v7.0.0_software/pipeline/mapping/bcSTAR: error while loading shared libraries: libnuma.so.1: cannot open shared object file: No such file or directory

RADIOMUMM commented 1 week ago

@RADIOMUMM Hi, you can be updated to SAW v7.0.1 to resolve it. Best wish!

Hi, I updated to SAW v7.0.1. But the error is still there.

/opt/saw_v7.0.0_software/pipeline/mapping/bcSTAR: error while loading shared libraries: libnuma.so.1: cannot open shared object file: No such file or directory

You need to go into the container and create a soft connection to libnuma.so.1.