ERROR : Failed to mount squashfs image in (read only): Invalid argument

[AntonioBaeza]

Admittedly, I am new to singularity, this is the error after installation:

(base) ant@hillary:~$ pwd /home/ant (base) ant@hillary:~$ (base) ant@hillary:~$ mkdir ~/dnaPipeTE (base) ant@hillary:~$ (base) ant@hillary:~$ cd dnaPipeTE/ (base) ant@hillary:~/dnaPipeTE$ (base) ant@hillary:~/dnaPipeTE$ pwd /home/ant/dnaPipeTE (base) ant@hillary:~/dnaPipeTE$ (base) ant@hillary:~/dnaPipeTE$ singularity pull --name dnapipete.img docker://clemgoub/dnapipete:latest WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/clemgoub/dnapipete:latest Cache folder set to /home/ant/.singularity/docker [30/30] |===================================| 100.0% Importing: base Singularity environment Exploding layer: sha256:bff3e048017eab8adaed886bad4b3c5c81f7d952b65b056dca8d6dbc198222dd.tar.gz Exploding layer: sha256:7454a22fef406b7c64195cfecc1f98bbf05d806c2fe8b2c090611d8174344152.tar.gz Exploding layer: sha256:48fbb22cd9b4218cb147f8c9289504463fab6fc409dd978ed2a41c74295209f1.tar.gz Exploding layer: sha256:e2d9047f3ead0e6275c786ee0c88173e9fda0a3c429090abd1a801459cf6318d.tar.gz Exploding layer: sha256:8a8adba02010309fedc1063050c516e399a57c40d0e82e6c6c353f345024a4de.tar.gz Exploding layer: sha256:ad67bcb30b6af5dabfa475f73bbe1aaf1598cd24db9260aec001a16fbecbdfa2.tar.gz Exploding layer: sha256:8ac634985821af7eea08a346f75053095514bad54749e5e2c2c1bb2beaddacad.tar.gz Exploding layer: sha256:70d11079cde67fb348435bfea1792e18b378183d7b2eb977551c2b0ac72c73ad.tar.gz Exploding layer: sha256:fbff193b270a70ae7eba474c4cdb74c717a225b28809fff0752d6e9ee262257e.tar.gz Exploding layer: sha256:bb765d177084f78bcc6ef19efec1e93505f7c503fab47ed8bd895f492d8bec30.tar.gz Exploding layer: sha256:68e8af20fafdc03b0c56c2a6b889be17bce6d1b78907f11416e07e42cabf3430.tar.gz Exploding layer: sha256:281a7872f45e4f1913a29ecdd7a25aac17bf0ff2cef68d2b65791b4d94c87913.tar.gz Exploding layer: sha256:3adbf49e1bc415c1cf93ce9d8bba2088795be2d5ff33a0f7664b7f36e2c24130.tar.gz Exploding layer: sha256:b285af44ce591fab52be4c2fc1586000d04484ed6d14f8cf8652706d146067e4.tar.gz Exploding layer: sha256:bc37b2c348d0bbcd24aba45a4419f1a9b9cc21a3ee28df50f719cd4ebc8b6c22.tar.gz Exploding layer: sha256:d3fd4fc0d24a0ab3ece78ae9609f71e5830fc6a2ea602f69c6f2405705175bff.tar.gz Exploding layer: sha256:ce2e9287fadac9a414fd1a74ed7e9e17dc7c7ded15e66bc9aaa7c4c1ba1f7c8e.tar.gz Exploding layer: sha256:57002df472312a576204b28a72ca44d6112cd9dfebef20f24a59ab7d6c0cf066.tar.gz Exploding layer: sha256:54b6d5886e3b906f0e69430a6e336d600fb226a38b530d0983877a56c380f5d3.tar.gz Exploding layer: sha256:48a0644ebad1664152f33805f5627d4cbf0f9919dec5347c467a95ae5b5318ee.tar.gz Exploding layer: sha256:c564aa69f587d709463c3bbe4105df3e933949db563345a3689e2c841c4b74cc.tar.gz Exploding layer: sha256:bf9e261ceb8d24afcf0b1733e7ec371cc5f1f97912113daebc535a5505eee9e2.tar.gz Exploding layer: sha256:b776c6dddc75f0a6191b4c30af093a50a9c6b40234a94ffc237a27f3071c18f0.tar.gz Exploding layer: sha256:045f6fa5b83ba7849563963a0a93136d2348ba887b89b6c814f5996bb79b23fa.tar.gz Exploding layer: sha256:9e53910bf641d9f7ba4e284afb4985084a767bf76e2ff0f269b339b7525462f1.tar.gz Exploding layer: sha256:13d2c9d56b9db4b5e0e390e30ab72c3a57b7d65cf070234c569a43ff832b5f9f.tar.gz Exploding layer: sha256:5042d36301999af1177e1a5857f318f52badaf23d9316fcc3aff0aadec07913e.tar.gz Exploding layer: sha256:443adbe8f68a9093d0e8277eb1b56d24d2f80aa20f0e97253ad945f7bef4039a.tar.gz Exploding layer: sha256:9942e1d2134458c4d649b74cbd0da41c14fe9b3469e9439b77b03c2593c9334a.tar.gz Exploding layer: sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1.tar.gz Exploding layer: sha256:438be21d4c5eb0e1f479b52707e9f06bc005e9f429061b11359a95791889981d.tar.gz WARNING: Building container as an unprivileged user. If you run this container as root WARNING: it may be missing some functionality. Building Singularity image... Singularity container built: ./dnapipete.img Cleaning up... Done. Container is at: ./dnapipete.img (base) ant@hillary:~/dnaPipeTE$ (base) ant@hillary:~/dnaPipeTE$ singularity shell ~/dnaPipeTE/dnapipete.img ERROR : Failed to mount squashfs image in (read only): Invalid argument ABORT : Retval = 255

[clemgoub]

Hello Antonio,

It may be that your version of singularity is too old. Can you check your current version is >= 3.5.3., and if necessary try to update with the latest?

Best,

Clément