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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Fatal error: Files compressed with gzip are not supported #446

Closed laaryjc closed 3 years ago

laaryjc commented 3 years ago

Hi, As per below, I keep getting this error. the wierd thing is it was workign last week, but now it won't progress. I have a fresh install of Conda, and even started again from scratch. Any thoughts?

[18:14:15] (base) laaryjc@HAL-at-AU:~/.ipyrad -p params_062921_micpet.txt -s 3 loading Assembly: micpet_LJC from saved path: ~/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC.json

ipyrad [v.0.9.81] Interactive assembly and analysis of RAD-seq data

Parallel connection | HAL-at-AU: 32 cores

Step 3: Clustering/Mapping reads within samples [####################] 100% 0:00:04 | join merged pairs

Encountered an Error. Message: IPyradError: Error merge pairs: ['/home/laaryjc/anaconda3/bin/vsearch', '--fastq_mergepairs', '/home/laaryjc/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC_edits/MP078.trimmedR1.fastq.gz', '--reverse', '/home/laaryjc/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC_edits/MP078.trimmedR2.fastq.gz', '--fastqout', '/home/laaryjc/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC-tmpalign/MP078_merged.fastq', '--fastqout_notmerged_fwd', '/home/laaryjc/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC-tmpalign/MP078_nonmergedR1.fastq', '--fastqout_notmerged_rev', '/home/laaryjc/Bioinformatics/Micpet_2021/iPyrad/micpet_LJC-tmpalign/MP078_nonmergedR2.fastq', '--fasta_width', '0', '--fastq_minmergelen', '35', '--fastq_maxns', '5', '--fastq_minovlen', '20', '--fastq_maxdiffs', '4', '--label_suffix', '_m1', '--fastq_qmax', '93', '--threads', '2', '--fastq_allowmergestagger'] vsearch v2.13.3_linux_x86_64, 78.6GB RAM, 32 cores https://github.com/torognes/vsearch

Fatal error: Files compressed with gzip are not supported

Parallel connection closed.

isaacovercast commented 3 years ago

Hm, that's weird. It looks like you're using an older version of vsearch that doesn't have zlib support. When I do vsearch -v on a working system I see this:

$ vsearch -v
vsearch v2.15.2_linux_x86_64, 251.8GB RAM, 40 cores
https://github.com/torognes/vsearch

Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016)
VSEARCH: a versatile open source tool for metagenomics
PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584

Compiled with support for gzip-compressed files, and the library is loaded.
zlib version 1.2.11, compile flags a9
Compiled with support for bzip2-compressed files, and the library is loaded.

I am pulling vsearch from bioconda, which you can see with conda list | grep vsearch

vsearch                   2.15.2               h2d02072_0    bioconda

You might try conda installing vsearch and using -c bioconda and --force-reinstall.

laaryjc commented 3 years ago

Ok, so prior to your comment i updated conda 3 times and the last time it caught the old vsearch and updated it to v2.17.1, but not the prior 2 times Weird indeed. thanks for the help!