Inputting Manifest File Error

[cgregg1227 (Collin Gregg)]

This is what I am inputting:
qiime2-2020.2) [mgcollin19@VME-PRD-HWL01 BCPE]$ qiime tools import \

--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /mnt/nfs/proj/bcp/Microbiome/16S/Data/BCPE/qiime2/BCPE_manifest3.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

This is the error message I keep getting:

Traceback (most recent call last):
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/util.py", line 89, in duplicate
os.link(src, dst)
OSError: [Errno 18] Invalid cross-device link: '/mnt/nfs/proj/bcp/Microbiome/16S/Data/BCPE/raw/MN0135A_16S_S187_R2_001.fastq.gz' -> '/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-jmqbf2ry/MN0135A_16S_S187__677_L001_R2_001.fastq.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 158, in import_data
view_type=input_format)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/result.py", line 241, in import_data
validate_level='max')
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/result.py", line 267, in _from_view
result = transformation(view, validate_level)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 445, in _25
single_end=False)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 299, in _fastq_manifest_helper
fastq_copy_fn(input_fastq_fp, str(output_fastq_fp))
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 272, in _copy_with_compression
qiime2.util.duplicate(src, dst)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/util.py", line 92, in duplicate
shutil.copyfile(src, dst)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/shutil.py", line 122, in copyfile
copyfileobj(fsrc, fdst)
File "/usr/local/miniconda2/envs/qiime2-2020.2/lib/python3.6/shutil.py", line 82, in copyfileobj
fdst.write(buf)
OSError: [Errno 28] No space left on device

An unexpected error has occurred:

[Errno 28] No space left on device

See above for debug info.

Any suggestions on what the issue might be?

Thank you,
Collin

[ChrisKeefe]

Hi @cgregg1227! Error messages aren't aways clear, but they're usually close enough to point you in the right direction. This forum's search tool is a great resource for troubleshooting stuff like this. Let's start with the error message that looks the most straightforward. We can look into other things if fixing this doesn't work.

@cgregg1227

[Errno 28] No space left on device

My guess here is that the system you're using either a) doesn't have enough storage space allocated for the import tool's file management needs, or the storage space it's trying to use is somewhere you don't have access to.

@jwdebelius did a great job with troubleshooting a very similar error here:

Manifest error problem

Hi @kimshinseung, It looks like you It looks like you’re out of space to write your manifest format. A couple things to check. First, make sure that you clean out your tmp directory. If you’re working on your local machine, you’re likely redirecting to a /tmp/ folder. You should empty that. If you’re on a cluster or server, talk to your sysadmin about where you should be sending your tmp data. (My sysadmin has occasionally been ready to kick me off the system for not using the appropriate tm…

Give it a shot, and let us know how it goes!

Best,
Chris