export error demultiplexed sequences

[Kendal_Morris]

Hi all,

I am getting an error after running the following:
(qiime2-2019.4) [email protected]:/media/sf_for_qiime2/spainCUE_v2$ qiime tools export --input-path demux_seqs.qza --output-path serenity_now

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.4/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 555, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 55, in export_data
result.export_data(output_path)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 137, in export_data
str(self._archiver.data_dir), str(output_dir))
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/distutils/dir_util.py”, line 163, in copy_tree
dry_run=dry_run)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/distutils/file_util.py”, line 158, in copy_file
os.utime(dst, (st[ST_ATIME], st[ST_MTIME]))
PermissionError: [Errno 1] Operation not permitted

In case you are curious, I looked at the file using validate. It looks good!

(qiime2-2019.4) [email protected]:/media/sf_for_qiime2/spainCUE_v2$ qiime tools validate demux_seqs.qza
Result demux_seqs.qza appears to be valid at level=max.

Any idea what could be going on?

Many thanks!
Kendal

[jwdebelius (Justine Debelius)]

Hi @Kendal_Morris,

I think you’re trying to move your sequences into a directory where you don’t have permission, either in your temp directory or in your serenity_now directory. What kind of system are you using?

Best,
Justine

[Kendal_Morris]

Hi Justine!

Very sorry for the slow response.

I am using a virtualbox set-up and the serenity_now folder is within my shared folder. Something interesting is that the folder appears and one of the files is successfully exported, but then the error is thrown.

[jwdebelius (Justine Debelius)]

Hi @Kendal_Morris,

No need to apologize for a weekend! They’re important.

Could you go to the directory above serenity_now and run ls -al on your parent folder and print the result?

Best,
Justine

[Kendal_Morris]

Hi @jwdebelius -

Here is the read out:

(qiime2-2019.4) [email protected]:/media/sf_for_qiime2/spainCUE_v2$ ls -altotal 988580
drwxrwx— 1 root vboxsf 20480 Jun 17 09:11 .
drwxrwx— 1 root vboxsf 12288 Jun 13 11:50 …
-rwxrwx— 1 root vboxsf 32004400 Feb 11 10:02 KM18_S25_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 37876253 Feb 11 10:02 KM18_S25_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 40841445 Feb 11 10:02 KM22_S26_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 48181576 Feb 11 10:02 KM22_S26_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 34912712 Feb 11 10:02 KM2_S23_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 40698819 Feb 11 10:02 KM2_S23_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 40762583 Feb 11 10:02 KM34_S27_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 47926175 Feb 11 10:02 KM34_S27_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 40967915 Feb 11 10:02 KM38_S28_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 48540023 Feb 11 10:02 KM38_S28_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 42985841 Feb 11 10:02 KM6_S24_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 50181023 Feb 11 10:02 KM6_S24_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 506041308 Jun 13 12:37 demux_seqs.qza
-rwxrwx— 1 root vboxsf 298112 Jun 13 12:39 demux_seqs.qzv
-rwxrwx— 1 root vboxsf 799 Jun 14 07:58 denoise.txt
drwxrwx— 1 root vboxsf 4096 Jun 13 12:57 ‘fastq pairedEnd’
drwxrwx— 1 root vboxsf 4096 Jun 13 12:55 ‘fastqc files’
-rwxrwx— 1 root vboxsf 375 Jun 13 12:58 firstContact.txt
drwxrwx— 1 root vboxsf 4096 Jun 13 12:55 ‘other copies of data’
-rwxrwx— 1 root vboxsf 875 Jun 13 12:36 spainCUE_pairedEnd.txt

[jwdebelius (Justine Debelius)]

Thanks @Kendal_Morris. It looks like your permissions are okay.
Do you know which file is passes before it fails? Like, you said one was working, is that consistent or is it a single file?

Thanks,
Justine

[Kendal_Morris]

Yes, it always passes the same file before crashing. I’ve put it in this google drive: https://drive.google.com/open?id=1UKznC9p8QCqpAi3XMG-N0-mz-uYrQNns

[jwdebelius (Justine Debelius)]

Cool! If it’s working, we probably don’t need to check it. Do you know which file fails? Like, Im guessing its this samples reverse read. If you load the reverse separately (as, say a single end Manifest), can you then export it?

Best,
Justine

[Kendal_Morris]

Hi Justine,
I haven’t tried your suggestion yet and in the interest of conserving everyone’s time (including my own) I’m going file this under Unsolved Mysteries for now, as there is no actual need to export files that I obviously already have individually.

Maybe I’ll come back to it in a few weeks when I’ve moved some other things off my plate.

Thanks again for your support!
Kendal