fastp
fastp copied to clipboard
OpenGene
Unable to download the latest version
Dear all,
I am using Mac M1 processor and it is giving me a hard time updating FASTP without conda. With conda I am able to update the FASTP however the latest version is 0.19
It will be admirable if you will be able to publish the latest version in conda as well.
Best regards and thank you.
Thank you for your email.
However, when running conda install -c bioconda fastp It's installing version 0.12.4-0
And while running conda install -c bioconda/label/cf201901 fastp It's installing version 0.19.5 As you can see: [image: image.png]
Both are not the latest version, and lacking some essential properties for my work.
I would highly appreciate your help!
Thank you
בתאריך יום א׳, 12 בדצמ׳ 2021 ב-13:01 מאת Shifu Chen < @.***>:
The latest version is already in Conda.
Each new fastp version is in Conda.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenGene/fastp/issues/383#issuecomment-991876527, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASVRHATUNK2JD6BOMUEXGEDUQR6IBANCNFSM5J4BLNTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
I have got exactly the same problem, the link above (despite what it says) does not install 0.23.2
@angusdavison Are you sure you're not seeing a dependency conflict? Fastq requires a newer version of libdeflate, which means that if you have e.g. BWA in your environment, you can't get the latest version of fastp.
Can you install it in an empty environment with nothing else it in?
I dont think that is the issue, though getting somewhat beyond my skills/knowledge. In any case, I installed the binaries via "wget http://opengene.org/fastp/fastp" - that is working fine. Thanks for your consideration
@angusdavison Are you sure you're not seeing a dependency conflict? Fastq requires a newer version of libdeflate, which means that if you have e.g. BWA in your environment, you can't get the latest version of fastp.
Can you install it in an empty environment with nothing else it in?
What libdeflate version does BWA use?
Looking at it for a bit more, I think the conflict is actually samtools not bwa, which needs htslib, which uses libdeflate 1.6, whereas fastp uses 1.7. But it's hard to know exactly.
Yes, agree there is probably a conflict but I don't know the source - a force install of 0.23.2 produced the following errors. Not sure if this is helpful or not (and I have got fastp working so I am not concerned)
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package libgcc-ng conflicts for: python=3.9 -> libgcc-ng[version='>=7.3.0|>=7.5.0'] python=3.9 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
Package libstdcxx-ng conflicts for: python=3.9 -> libstdcxx-ng[version='>=7.3.0|>=7.5.0'] fastp=0.23.2 -> libstdcxx-ng[version='>=9.4.0']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.17
But fastp dons't declare a dependency on libstdcxx-ng[version='>=9.4.0'].
I checked annocanda, the latest version for libstdcxx-ng is 9.3.0.
Hello. Unfortunately, I am also having some install issues.
"conda install -c bioconda fastp" installs version 0.12.4
"conda install -c bioconda/label/cf201901 fastp" installs version 0.19.5
I would like to use these two arguments: --detect_adapter_for_pe and --cut_tail. However, it looks like --detect_adapter_for_pe isn't in 0.12.4 and --cut_tail isn't in 0.19.5. As an example, I get the message "undefined option: --cut_tail"
I created a new conda environment to ensure there were no conflicts and the problem is still there. I am running conda 4.11.0 on OSX through terminal.
Any guidance would be appreciated. Thanks!
Hello again. Just wanted to provide an update for those looking for a workaround. I was able to install an older version of fastp by downloading the file from conda and running: "conda install fastp-0.20.0-hd9629dc_0.tar.bz2". I was then able to use the two arguments I wanted. Importantly, it wouldn't work on the university cluster for some reason (cannot execute binary file) but it worked on my work macbook. I tried it the same thing with the latest version 0.23.2 but it didn't work (dyld: Library not loaded: @rpath/libisal.2.dylib). Just trialling a few more: version 0.23.0 also didn't work with this method but 0.22.0 did.
Thanks!
I am also having an issue with fastp where it wont write cleaned reads. Using the basic commands with paired end data, fastp only writes QC reports. I know there are good reads for all the sequences when reading the the json & html outputs; but this is a seperate issue. To solve this, I thought I would try updating it to the latest version since I realized I did not have the latest. However, I cannot install the latest 0.23.# or even 0.22.# versions
conda install -c bioconda/label/cf201901 installs fastp-0.19.5 conda install -c bioconda/label/main installs fastp-0.20.1 conda install -c bioconda fastp installs fastp-0.20.1
I've tried various conda install commands to force install the absolute latest version "fastp=0.23.2". I've used a fresh conda environment with different python versions. At this point I'm not sure what to do.
@Jediworm
I wonder if this workaround is OK if you have sudo permissions. I've tried downloading it to my home dir on the cluster I use and installing from there.
$ fastp -v
fastp: error while loading shared libraries: libisal.so.2: cannot open
shared object file: No such file or directory
From my novice understanding, don't I need to download the tarball to the anaconda package directory? (/local/anaconda3/pkgs/); and then "conda install /local/anaconda3/pkgs/fastp-...." ?
A workaround would be creating a new conda environment and installing the latest fastp.
conda create -n fastp -c bioconda fastp=0.23.2
I have the same issue, solved by setting the environment variable. export LD_LIBRARY_PATH=" your libdeflate path containing the file libdeflate.so.0" I wonder this is caused by makefile
