Error with qiime tools import

[pyilmaz]

I’m having some issues with import which I’m not sure what’s it due to. I’m trying to import two fastq files, demultiplexed, paired end:

qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path /home/pyilmaz/myOSD16/test/test-manifest --source-format PairedEndFastqManifestPhred33 --output-path /home/pyilmaz/myOSD16/test/test_output.qza

In return I get this error:

    Traceback (most recent call last):
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/bin/qiime", line 6, in <module>
       sys.exit(q2cli.__main__.qiime())
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 722, in __call__
       return self.main(*args, **kwargs)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 697, in main
       rv = self.invoke(ctx)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
       return _process_result(sub_ctx.command.invoke(sub_ctx))
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
       return _process_result(sub_ctx.command.invoke(sub_ctx))
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 895, in invoke
       return ctx.invoke(self.callback, **ctx.params)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/click/core.py", line 535, in invoke
       return callback(*args, **kwargs)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/q2cli/tools.py", line 62, in import_data
       view_type=source_format)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 191, in import_data
       return cls._from_view(type_, view, view_type, provenance_capture)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 216, in _from_view
       result = transformation(view)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in transformation
       new_view = transformer(view)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 355, in _8
       return _fastq_manifest_helper(fmt, os.link, single_end=False)
     File "/home/pyilmaz/sandbox/miniconda2/envs/qiime2-2017.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 317, in _fastq_manifest_helper
       fastq_copy_fn(input_fastq_fp, str(output_fastq_fp))
    OSError: [Errno 18] Invalid cross-device link: '/home/pyilmaz/myOSD16/test/MYOSD681_2016-06-1_R1.fastq.gz' -> '/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-5y79_frg/sample-1_0_L001_R1_001.fastq.gz'

Thanks for your suggestions!

[ebolyen (Evan Bolyen)]

Thanks @pyilmaz!

It looks like you found a bug/unsupported feature. QIIME 2 doesn’t seem to understand cross-device filesystems. No reason it can’t, but it’s not clever enough yet to back out and perform a copy.

What you can do in the meanwhile is to ensure your data is on the same physical device as your temporary directory (either change your temporary directory with an environment variable, or move your files). Your sys-admin can probably help you there. Otherwise, I’ve created an issue to track this.