Out of disk space error

User Support
1

Hi,
I encountered another issue when I want to downloaded all my samples I received this error:
qiime tools import \

–type ‘SampleData[PairedEndSequencesWithQuality]’ \

–input-path /mnt/beegfs/scratch/eh309/170818_lane2/trimmed/manifest_uganda.txt \

–output-path demux.qza \

–source-format PairedEndFastqManifestPhred33

An unexpected error has occurred:

[Errno 28] No space left on device

I created then a new temporary environment variable then I had this error: An unexpected error has occurred:

[Errno 17] File exists: ‘/mnt/beegfs/scratch/eh309/170818_lane2/trimmed/q2-SingleLanePerSamplePairedEndFastqDirFmt-lagv1oap’ -> ‘/mnt/beegfs/scratch/eh309/170818_lane2/trimmed/qiime2-archive-tmm10xqb/859d5f26-bb22-4fc6-ad3b-d3e0b69a8b5a/data’

Do you have any idea?
Many thanks for your help.
Hajar

3

Hey there @Hajar!

This means that the partition you are working on has run out of disk space. Can you run the following and share the output:

df -h

This looks a lot like this issue:

Pinging @ebolyen

6

Thanks for your quick reply,

Here is the outcomes from df -h:
[eh309@gm-hpc-login-01 trimmed]$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 20G 15G 5.3G 74% /
devtmpfs 63G 0 63G 0% /dev
tmpfs 63G 194M 63G 1% /run
tmpfs 63G 62G 1.6G 98% /dev/shm
tmpfs 63G 0 63G 0% /sys/fs/cgroup
/dev/sda6 183G 79G 104G 44% /local
/dev/sda3 2.0G 1.8G 206M 90% /tmp
/dev/sda2 6.0G 938M 5.1G 16% /var
master:/home 429G 415G 15G 97% /home
master:/cm/shared 429G 415G 15G 97% /cm/shared
tmpfs 13G 12K 13G 1% /run/user/42
beegfs_nodev 350T 57T 293T 17% /mnt/beegfs
tmpfs 13G 4.0K 13G 1% /run/user/1991606411
tmpfs 13G 0 13G 0% /run/user/1991666062
tmpfs 13G 0 13G 0% /run/user/1991666384

I changed my environment variables TMPDIR to a hard disk of my HPC account then I progressed with dada2. However, I got stuck with another error [Errno 17] File exists. Here the steps:

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0

  1. Filtering
    …

  2. Learning Error Rates
    2a) Forward Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 354502 reads in 31019 unique sequences.
    Sample 2 - 400996 reads in 45831 unique sequences.
    Sample 3 - 607285 reads in 56126 unique sequences.
    selfConsist step 2
    selfConsist step 3
    selfConsist step 4
    Convergence after 4 rounds.
    2b) Reverse Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 354502 reads in 39752 unique sequences.
    Sample 2 - 400996 reads in 60974 unique sequences.
    Sample 3 - 607285 reads in 75674 unique sequences.
    selfConsist step 2
    selfConsist step 3
    selfConsist step 4
    selfConsist step 5
    Convergence after 5 rounds.

  3. Denoise remaining samples …
    The sequences being tabled vary in length.

  4. Remove chimeras (method = consensus)

  5. Write output

[Errno 17] File exists

Then the filtering process was interrupted and no output files were generated.
Is that because of space issue? Although the bioinformatic team said that I don’t have any CPU restrictions, I am still receiving this error.
Any advice is highly appreciated.

7

Hi,
Glad to let you know that the command worked when I added --p-n-threads 0 \ , below is the full command I used:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-n-threads 0
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 250
–p-trunc-len-r 250
–o-table table.qza
–o-representative-sequences seqs.qza
–verbose
–o-denoising-stats denoising-stats.qza
qiime feature-table summarize
–i-table table.qza
–o-visualization table.qzv \

thanks a lot.
Hajar

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9

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