[ErrNo 17] file exists during classify

Hi all,

I’ve run into an issue trying to use feature-classifier classify-sklearn to assign taxonomy to my rep-seqs.qza file. Similar to this thread, I had to set my bash $TMPDIR to network attached storage partition on my cluster after receiving this message:

plugin error from feature-classifier:
[Errno 28] No space left on device

After setting $TMPDIR, the feature-classifier classify-sklearn command ran fine for about four hours, and then quit displaying this error message:

plugin error from feature-classifier:

[Errno 17] File exists: ‘/home/mingala/nas1/q2-TSVTaxonomyDirectoryFormat-vaipuhmk’ -> '/home/mingala/nas1/qiime2-archive-e3rhddal/$

Debug info has been saved to /home/mingala/nas1/qiime2-q2cli-err-el67bl1g.log

However, when I search the output directory, that file does not exist! Any idea what might be causing this issue?

Hi @mingala,

Sorry for the delay on my part.

I’ve seen something similar to this once: Qiime2 installation and run error
and to be honest, I still don’t understand what is going on with that.

What does

mount

display (in particular for nas1)?

What’s even more unfortunate is it appears your command had more or less finished, but something about the archive it was preparing either didn’t exist, had the wrong permissions, or failed to be mounted in a writable way?

Hi @ebolyen,

Thanks for your reply; I was traveling and have just arrived back to work on this issue.

When I cd into nas1/ and run

mount

I get the following:

[[email protected] (cuvier):~] $ cd nas1/

[[email protected] (cuvier):~/nas1] $ mount

sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)

proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)

devtmpfs on /dev type devtmpfs (rw,nosuid,size=528245084k,nr_inodes=132061271,mode=755)

securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)

tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)

devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)

tmpfs on /run type tmpfs (rw,nosuid,nodev,mode=755)

tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)

cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/usr/lib/systemd/systemd-cgroups-agent,name=systemd)

pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)

cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)

cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)

cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)

cgroup on /sys/fs/cgroup/hugetlb type cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)

cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)

cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpuacct,cpu)

cgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)

cgroup on /sys/fs/cgroup/net_cls,net_prio type cgroup (rw,nosuid,nodev,noexec,relatime,net_prio,net_cls)

cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)

cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)

configfs on /sys/kernel/config type configfs (rw,relatime)

/dev/mapper/vg–local-lv–root on / type ext4 (rw,relatime,stripe=64,data=ordered)

/dev/mapper/vg–local-lv–usr on /usr type ext4 (rw,relatime,stripe=64,data=ordered)

systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=34,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=21722)

debugfs on /sys/kernel/debug type debugfs (rw,relatime)

hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)

mqueue on /dev/mqueue type mqueue (rw,relatime)

/dev/sda1 on /boot type ext4 (rw,relatime,stripe=256,data=ordered)

/dev/mapper/vg–local-lv–usr–local on /usr/local type ext4 (rw,relatime,stripe=64,data=ordered)

/dev/mapper/vg–local-lv–var on /var type ext4 (rw,relatime,stripe=64,data=ordered)

/dev/mapper/vg–local-lv–tmp on /tmp type ext4 (rw,relatime,stripe=64,data=ordered)

/dev/mapper/vg–local-lv–database on /database type ext4 (rw,relatime,stripe=64,data=ordered)

/dev/mapper/vg–local-lv–home on /home type ext4 (rw,relatime,quota,usrquota,grpquota,stripe=64,data=ordered)

/dev/mapper/vg–das-lv–data1 on /data1 type xfs (rw,relatime,attr2,inode64,logbsize=256k,sunit=512,swidth=7168,noquota)

/dev/mapper/vg–das-lv–array1 on /array1 type xfs (rw,relatime,attr2,inode64,logbsize=256k,sunit=512,swidth=7168,usrquota)

sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw,relatime)

binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,relatime)

gen-nas.internal.amnh.org:/nas1 on /nas1 type nfs (rw,relatime,vers=3,rsize=32768,wsize=32768,namlen=255,soft,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=172.16.9.82,mountvers=3,mountport=2049,mountproto=udp,local_lock=none,addr=172.16.9.82,_netdev)

gen-nas.internal.amnh.org:/nas2 on /nas2 type nfs (rw,relatime,vers=3,rsize=32768,wsize=32768,namlen=255,soft,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=172.16.9.82,mountvers=3,mountport=2049,mountproto=udp,local_lock=none,addr=172.16.9.82,_netdev)

Not sure if any of that is helpful! Yes, I was also troubled to see that the code almost executed properly, which made the error that much more difficult to understand.

Hey there @mingala!

It looks like /nas1 is a network-mounted NFS drive:

My guess is that there is a driver or compatibility error happening here - it looks like the filesystem (and its metadata) is temporarily in an inconsistent state. This would be a good one to send towards your cluster sysadmin, they might have some ideas. I don’t think this is a QIIME 2 error at this point, I think this has to do with the filesystem (either the local mount, or maybe on the NFS server…).

Please keep us posted. :t_rex:

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