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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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Docker fails to mount HD_DIR #3

Closed alkminion1 closed 2 years ago

alkminion1 commented 2 years ago

Hi! The following error occurs when I try to run:

sudo docker run -v $HD_DIR:$HD_DIR -u `id -u`:`id -g` mkolmogo/hapdup:0.2   hapdup --assembly $HD_DIR/barcode11CBS1878_v2.fasta --bam $HD_DIR/lr_mapping.bam --out-dir $HD_DIR/hapdup
docker: Error response from daemon: error while creating mount source path '/home/user/data/volume_2/hapdup_results': mkdir /home/user/data: file exists.
ERRO[0000] error waiting for container: context canceled``
mikolmogorov commented 2 years ago

Hi,

Something is wrong with the directory mounting. Could you give us more information about your OS?

Also (1) try without sudo, (2) with -v /home:/home, (3) post the output of df -h

@kishwarshafin any ideas?

alkminion1 commented 2 years ago

Hi! thank you for your reply!

My OS is Ubuntu 18.04.6 LTS (GNU/Linux 4.15.0-159-generic x86_64)

  1. Without sudo I get 

    docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create": dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'.

  2. with -v /home:/home I get:

    Traceback (most recent call last):
File "/usr/local/bin/hapdup", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 53, in main
os.mkdir(args.out_dir)
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/data/volume_2/hapdup_results/hapdup'

    even after I tried mkdir hapdup

  3. df -h output is:

    Filesystem      Size  Used Avail Use% Mounted on
udev             16G     0   16G   0% /dev
tmpfs           3.2G  1.1M  3.2G   1% /run
/dev/sda1        15G   12G  3.3G  78% /
tmpfs            16G     0   16G   0% /dev/shm
tmpfs           5.0M     0  5.0M   0% /run/lock
tmpfs            16G     0   16G   0% /sys/fs/cgroup
/dev/sda15      105M  6.7M   98M   7% /boot/efi
/dev/sdb1      1000G  241G  760G  25% /data/volume_2
tmpfs           3.2G     0  3.2G   0% /run/user/1002
/dev/loop0       33M   33M     0 100% /snap/snapd/13640
/dev/loop1       56M   56M     0 100% /snap/core18/2246
/dev/loop2      117M  117M     0 100% /snap/docker/1125
/dev/loop3       43M   43M     0 100% /snap/snapd/13831
mikolmogorov commented 2 years ago

Ok, I think the issue is that you have a symlink in your HD_DIR, that is pointing to /data/volume_2 and is not correctly resolved by Docker. Let's try the following:

  1. In your original HD_DIR, run HD_DIR=$(realpath $(pwd)).

  2. Post output of echo $HD_DIR

  3. The Docker command from the manual should work now.

  4. Alternatively, you could also try to cd into HD_DIR using the real mount path (e.g. cd /data/volume_2/...), and then repeat the original instructions from the manual.

mikolmogorov commented 2 years ago

And if the tips above fail, please post output of docker run -v "/:/host" busybox df -h

alkminion1 commented 2 years ago

  1. With HD_DIR=$(realpath $(pwd)) I got a similar error:

    docker: Error response from daemon: error while creating mount source path '/data/volume_2/hapdup_results': mkdir /data: read-only file system.
ERRO[0000] error waiting for container: context canceled

  2. echo $HD_DIR outputs /data/volume_2/hapdup_results

  3. the output of sudo docker run -v "/:/host" busybox df -h (again permission error w/out sudo)

    Unable to find image 'busybox:latest' locally
latest: Pulling from library/busybox
e685c5c858e3: Pull complete
Digest: sha256:e7157b6d7ebbe2cce5eaa8cfe8aa4fa82d173999b9f90a9ec42e57323546c353
Status: Downloaded newer image for busybox:latest
Filesystem                Size      Used Available Use% Mounted on
overlay                  14.4G     11.1G      3.2G  78% /
tmpfs                    64.0M         0     64.0M   0% /dev
tmpfs                    15.7G         0     15.7G   0% /sys/fs/cgroup
shm                      64.0M         0     64.0M   0% /dev/shm
/dev/loop1               55.5M     55.5M         0 100% /host
udev                     15.7G         0     15.7G   0% /host/dev
tmpfs                    15.7G         0     15.7G   0% /host/dev/shm
/dev/sda1                15.7G         0     15.7G   0% /host/etc
/dev/loop1               55.5M     55.5M         0 100% /host/etc/nsswitch.conf
/dev/loop1               55.5M     55.5M         0 100% /host/etc/apparmor
/dev/loop1               55.5M     55.5M         0 100% /host/etc/apparmor.d
tmpfs                    15.7G         0     15.7G   0% /host/etc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/.java
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/.pwd.lock
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/NetworkManager
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/X11
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/acpi
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/adduser.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/alternatives
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/apache2
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/apm
/dev/loop1               55.5M     55.5M         0 100% /host/etc/apparmor
/dev/loop1               55.5M     55.5M         0 100% /host/etc/apparmor.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/apport
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/apt
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/at.deny
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/bash.bashrc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/bash_completion
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/bash_completion.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/bindresvport.blacklist
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/binfmt.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/blends
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/byobu
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ca-certificates
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ca-certificates.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ca-certificates.conf.dpkg-old
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/calendar
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cloud
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/console-setup
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cron.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cron.daily
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cron.hourly
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cron.monthly
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cron.weekly
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/crontab
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/cryptsetup-initramfs
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/crypttab
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/davfs2
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dbus-1
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/debconf.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/debian_version
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/default
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/deluser.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/depmod.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dhcp
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dictionaries-common
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dnsmasq.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dnsmasq.d-available
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/dpkg
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ec2_version
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/emacs
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/environment
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ethertypes
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/fail2ban
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/fonts
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/fstab
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/fuse.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gai.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gdb
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/glvnd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/groff
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/group
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/group-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/grub.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gshadow
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gshadow-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gss
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gtk-2.0
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gtk-3.0
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/hdparm.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/host.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/hostname
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/hosts
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/hosts.allow
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/hosts.deny
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/init.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/initramfs-tools
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/inputrc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/iproute2
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/iscsi
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/issue
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/issue.net
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/java-11-openjdk
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/kernel
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/kernel-img.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/landscape
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ld.so.cache
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ld.so.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ld.so.conf.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ldap
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/legal
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/libaudit.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/libgda-5.0
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/lighttpd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/locale.alias
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/locale.gen
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/logcheck
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/login.defs
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/logrotate.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/logrotate.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/lsb-release
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ltrace.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/lvm
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/machine-id
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/magic
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/magic.mime
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/mailcap
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/mailcap.order
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/manpath.config
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/mdadm
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/menu
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/menu-methods
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/mime.types
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/mke2fs.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/modprobe.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/modules
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/modules-load.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/monit
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/nanorc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ncbi
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/netplan
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/network
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/networkd-dispatcher
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/networks
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/newt
/dev/loop1               55.5M     55.5M         0 100% /host/etc/nsswitch.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/opt
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/overlayroot.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/overlayroot.local.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/pam.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/pam.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/passwd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/passwd-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/perl
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/pm
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/polkit-1
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/pollinate
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/popularity-contest.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/profile
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/profile.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/protocols
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/pulse
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/python
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/python2.7
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/python3
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/python3.6
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc0.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc1.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc2.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc3.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc4.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc5.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rc6.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rcS.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rmt
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rpc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rsc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rsyslog.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/rsyslog.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/screenrc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/securetty
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/security
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/selinux
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sensors.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sensors3.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/services
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/shadow
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/shadow-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/shells
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/skel
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sos
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sos.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ssh
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ssl
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/su-to-rootrc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/subgid
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/subgid-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/subuid
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/subuid-
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sudoers
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sudoers.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sysctl.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/sysctl.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/systemd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/terminfo
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/timezone
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/tmpfiles.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ubuntu-advantage
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ucf.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/udev
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/ufw
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/update-manager
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/update-motd.d
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/updatedb.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/vim
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/vmware-tools
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/wgetrc
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/xdg
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/zsh_command_not_found
/dev/sda1                14.4G     11.1G      3.2G  78% /host/etc/gitconfig
/dev/sda1                14.4G     11.1G      3.2G  78% /host/home
/dev/sda1                14.4G     11.1G      3.2G  78% /host/root
tmpfs                    15.7G         0     15.7G   0% /host/sys/fs/cgroup
/dev/sda1                14.4G     11.1G      3.2G  78% /host/tmp
/dev/sda1                14.4G     11.1G      3.2G  78% /host/tmp
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/snap
overlay                  14.4G     11.1G      3.2G  78% /host/var/snap/docker/common/var-lib-docker/overlay2/8a236400e2dfe09b89371870e6f2ff51af9f64512c970a406c7d0e138f4a3760/merged
overlay                  14.4G     11.1G      3.2G  78% /host/var/snap/docker/common/var-lib-docker/overlay2/8a236400e2dfe09b89371870e6f2ff51af9f64512c970a406c7d0e138f4a3760/merged
tmpfs                    64.0M         0     64.0M   0% /host/var/snap/docker/common/var-lib-docker/overlay2/8a236400e2dfe09b89371870e6f2ff51af9f64512c970a406c7d0e138f4a3760/merged/dev
shm                      64.0M         0     64.0M   0% /host/var/snap/docker/common/var-lib-docker/overlay2/8a236400e2dfe09b89371870e6f2ff51af9f64512c970a406c7d0e138f4a3760/merged/dev/shm
tmpfs                    15.7G         0     15.7G   0% /host/var/snap/docker/common/var-lib-docker/overlay2/8a236400e2dfe09b89371870e6f2ff51af9f64512c970a406c7d0e138f4a3760/merged/sys/fs/cgroup
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/lib/snapd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/lib/snapd/hostfs
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/lib/snapd/hostfs
tmpfs                     3.1G      1.1M      3.1G   0% /host/var/lib/snapd/hostfs/run
tmpfs                     5.0M         0      5.0M   0% /host/var/lib/snapd/hostfs/run/lock
tmpfs                     3.1G         0      3.1G   0% /host/var/lib/snapd/hostfs/run/user/1002tmpfs                     3.1G      1.1M      3.1G   0% /host/var/lib/snapd/hostfs/run/snapd/ns
/dev/sda15              104.4M      6.7M     97.7M   6% /host/var/lib/snapd/hostfs/boot/efi
/dev/sdb1               999.5G    236.9G    762.7G  24% /host/var/lib/snapd/hostfs/data/volume_2/dev/loop0               32.5M     32.5M         0 100% /host/var/lib/snapd/hostfs/snap/snapd/13640
/dev/loop1               55.5M     55.5M         0 100% /host/var/lib/snapd/hostfs/snap/core18/2246
/dev/loop2              116.6M    116.6M         0 100% /host/var/lib/snapd/hostfs/snap/docker/1125
/dev/loop3               42.3M     42.3M         0 100% /host/var/lib/snapd/hostfs/snap/snapd/13831
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/tmp
tmpfs                     3.1G      1.1M      3.1G   0% /host/run
tmpfs                     5.0M         0      5.0M   0% /host/run/lock
tmpfs                     3.1G         0      3.1G   0% /host/run/user/1002
tmpfs                     3.1G      1.1M      3.1G   0% /host/run/snapd/ns
tmpfs                     3.1G      1.1M      3.1G   0% /host/run/netns
/dev/sda1                14.4G     11.1G      3.2G  78% /host/lib/modules
/dev/sda1                14.4G     11.1G      3.2G  78% /host/usr/src
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/log
/dev/sda1                14.4G     11.1G      3.2G  78% /host/media
/dev/sda1                14.4G     11.1G      3.2G  78% /host/mnt
/dev/loop0               32.5M     32.5M         0 100% /host/usr/lib/snapd
/dev/sda1                14.4G     11.1G      3.2G  78% /host/snap
/dev/loop0               32.5M     32.5M         0 100% /host/snap/snapd/13640
/dev/loop1               55.5M     55.5M         0 100% /host/snap/core18/2246
/dev/loop2              116.6M    116.6M         0 100% /host/snap/docker/1125
/dev/loop3               42.3M     42.3M         0 100% /host/snap/snapd/13831
tmpfs                    15.7G         0     15.7G   0% /host/usr/lib
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/NetworkManager
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/binfmt.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/cloud-init
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/core18
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/dbus-1.0
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/environment.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/finalrd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/gcc
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/i386-linux-gnu
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/initramfs-tools
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/kernel
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/libnss_extrausers.so.2
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/locale
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/mime
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/modules-load.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/openssh
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/os-release
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/pm-utils
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/python3
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/python3.6
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/python3.7
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/python3.8
/dev/loop0               32.5M     32.5M         0 100% /host/usr/lib/snapd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/ssl
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/sudo
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/sysctl.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/systemd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/sysusers.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/tar
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/tc
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/tmpfiles.d
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/valgrind
/dev/loop1               55.5M     55.5M         0 100% /host/usr/lib/x86_64-linux-gnu
tmpfs                    15.7G         0     15.7G   0% /host/usr/share
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/adduser
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/applications
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/apport
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/base-files
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/base-passwd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/bash-completion
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/binfmts
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/bug
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/ca-certificates
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/cmake
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/common-licenses
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/dbus-1
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/debianutils
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/dict
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/distro-info
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/doc
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/doc-base
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/dpkg
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/finalrd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/fonts
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/gcc-8
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/gdb
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/glib-2.0
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/icons
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/info
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/initramfs-tools
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/iptables
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/keyrings
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/libc-bin
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/lintian
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/locale
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/man
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/menu
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/misc
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/netplan
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/openssh
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/pam
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/pam-configs
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/perl5
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/pixmaps
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/pkgconfig
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/polkit-1
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/probert
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/python3
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/readline
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/sensible-utils
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/snappy
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/subiquity
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/systemd
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/tabset
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/terminfo
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/vim
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/zoneinfo
/dev/loop1               55.5M     55.5M         0 100% /host/usr/share/zsh
/dev/sda1                14.4G     11.1G      3.2G  78% /host/var/lib/dhcp
/dev/sda1                14.4G     11.1G      3.2G  78% /etc/resolv.conf
/dev/sda1                14.4G     11.1G      3.2G  78% /etc/hostname
/dev/sda1                14.4G     11.1G      3.2G  78% /etc/hosts
tmpfs                    15.7G         0     15.7G   0% /proc/acpi
tmpfs                    64.0M         0     64.0M   0% /proc/kcore
tmpfs                    64.0M         0     64.0M   0% /proc/keys
tmpfs                    64.0M         0     64.0M   0% /proc/timer_list
tmpfs                    64.0M         0     64.0M   0% /proc/sched_debug
tmpfs                    15.7G         0     15.7G   0% /proc/scsi
tmpfs                    15.7G         0     15.7G   0% /sys/firmware

  4. no difference

mikolmogorov commented 2 years ago

@alkminion1 Ok, so the df -h output does not look right to me. And as you can see /data/volume_2 not mounted, even though it should. Might be some issues with the mounting options.

I suspect this is something to do with your Docker / OS configuration, so my help is limited here. You can try the following though:

  1. Try using filesystem other than /data/volume_2, e.g. your /home filesystem seems to be mounted correctly.
  2. Reinstall Docker and make sure it's properly configured, e.g. you can run it without sudo
  3. Try Singularity instead (see new instructions in the README)
kishwarshafin commented 2 years ago

@alkminion1 I'm afraid that you are not mounting the input/output directories correctly. One way to make it simpler is to copy all of your input files into a single directory like this:

INPUT_DIR=/data/volume_2/hapdup_inputs
OUTPUT_DIR=/data/volume_2/hapdup_inputs/hapdup_output
mkdir -p "${INPUT_DIR}"
mkdir -p "${OUTPUT_DIR}"

cp /data/volume_2/hapdup_results/barcode11CBS1878_v2.fasta "${INPUT_DIR}"
cp /data/volume_2/hapdup_results/barcode11CBS1878_v2.fasta.fai "${INPUT_DIR}"
cp /data/volume_2/hapdup_results/lr_mapping.bam "${INPUT_DIR}"
cp /data/volume_2/hapdup_results/lr_mapping.bam.bai "${INPUT_DIR}"
INPUT_FASTA="${INPUT_DIR}"/barcode11CBS1878_v2.fasta 
INPUT_BAM="${INPUT_DIR}"/lr_mapping.bam

docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
-u `id -u`:`id -g` \
mkolmogo/hapdup:0.2  hapdup \
--assembly "${INPUT_FASTA}" \
--bam "${INPUT_BAM}" \
--out-dir "${OUTPUT_DIR}"

Hopefully this will work

mikolmogorov commented 2 years ago

Closed due to inactivity. Feel free to follow up if the problem remains.