Hi folks,
I am trying to denoise a demux file. The demux file was made from 48 fastq files that look just like a regular fastq file but am starting with reads from which the primer/adapters were already cut out using cutadapt. I don't usually do it this way but someone did it this for me to help out with difficult removal of primers/adapters (something weird happened during the sequence run). When I run denoising I get a message stating that my file is not a Qiime artifact (see below), yet the demultiplexing seems to work just fine. I used Qiime tools validate on the demultiplexed file and the message (also below) seems to indicate that it "sees" gz files, which is a little confusing because I had gunzipped the files before demultiplexing (or so I thought). This was done within QIIME2 2019.10 on the cyverse platform (I am checking with them too just in case there is an issue with this app). Any thoughts on what might be going on here?
Alternatively, if anyone has a recommendation of another way I could quickly get repseqs and table, that would be great as a quick fix. I have no fancy analysis in mind, I just need to repseqs so that I can search against NCBI. In the long run it looks like I should switch to Docker. Thanks for any suggestions!
Bill
DADA2 COMMAND AND ERROR
I am using qiime2.2019.10 in cyverse but this seems to be an issue with every version in cyverse.
!qiime dada2 denoise-single
--i-demultiplexed-seqs /filepath/file.qza
--p-trunc-len 0
--p-trim-left 0
--p-max-ee 1
--o-table /filepath/table
--o-representative-sequences /filepath/repseqs
--o-denoising-stats /filepath/denoise
(1/1) Invalid value for "--i-demultiplexed-seqs": '/filepath/file.qza' is not a QIIME 2 Artifact (.qza)
QIIME TOOLS VALIDATE RESULTS
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 409, in validate
result = qiime2.sdk.Result.load(path)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/result.py", line 66, in load
archiver = archive.Archiver.load(filepath)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 305, in load
rec = archive.mount(path)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 204, in mount
root = self.extract(filepath)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/core/archive/archiver.py", line 215, in extract
zf.extract(name, path=str(filepath))
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/zipfile.py", line 1507, in extract
return self._extract_member(member, path, pwd)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/zipfile.py", line 1579, in _extract_member
shutil.copyfileobj(source, target)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/shutil.py", line 79, in copyfileobj
buf = fsrc.read(length)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/zipfile.py", line 872, in read
data = self._read1(n)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/zipfile.py", line 962, in _read1
self._update_crc(data)
File "/opt/conda/envs/qiime2-2019.10/lib/python3.6/zipfile.py", line 890, in _update_crc
raise BadZipFile("Bad CRC-32 for file %r" % self.name)
zipfile.BadZipFile: Bad CRC-32 for file '7694313a-fa5d-4208-bcd8-bc6e5685ebe7/data/T2163_8_L001_R1_001.fastq.gz'
There was a problem loading /data-store/iplant/home/wlandesman/RO3-Plate4/12S-Trimmed-Nov5/demux-trimmed-nov5.qza as a QIIME 2 Result:
Bad CRC-32 for file '7694313a-fa5d-4208-bcd8-bc6e5685ebe7/data/T2163_8_L001_R1_001.fastq.gz'
See above for debug info.