Segmentation fault 11 with bioconda build

[dougbarrows]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? salmon

Describe the bug A clear and concise description of what the bug is.

I had an older version of salmon that works (v0.8.2) that I believe was not compiled with Bioconda. I am now trying to get the latest version through Bioconda and with the same "salmon quant" command (See below) that works on the old version, I get a "segmentation fault 11" error and it never actually quantifies any reads. Do you know why this would happen?

To Reproduce Steps and data to reproduce the behavior:

Specifically, please provide at least the following information:

• Which version of salmon was used? 0.11.3
• How was salmon installed (compiled, downloaded executable, through bioconda)? Bioconda
• Which reference (e.g. transcriptome) was used? gencode.v27.transcripts.fa
• Which read files were used? fastq
• Which which program options were used? -l A, single end

Screenshots If applicable, add screenshots or terminal output to help explain your problem.

salmon quant -i ~/Reference_indexes/humangencodev27_transcripts_index_20181023 -l A -r ~/Downloads/ENCFF600FYP.fastq.gz -o ./salmon_test/ENCFF600FYP_quant
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v0.11.3
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { ~/Reference_indexes/humangencodev27_transcripts_index_20181023 }
### [ libType ] => { A }
### [ unmatedReads ] => { ~/Downloads/ENCFF600FYP.fastq.gz }
### [ output ] => { ./salmon_test/ENCFF600FYP_quant }
Logs will be written to ./salmon_test/ENCFF600FYP_quant/logs
[2018-10-23 20:11:13.424] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2018-10-23 20:11:13.425] [jointLog] [info] parsing read library format
[2018-10-23 20:11:13.425] [jointLog] [info] There is 1 library.
[2018-10-23 20:11:13.513] [stderrLog] [info] Loading Suffix Array 
[2018-10-23 20:11:13.513] [jointLog] [info] Loading Quasi index
[2018-10-23 20:11:13.513] [jointLog] [info] Loading 32-bit quasi index
[2018-10-23 20:11:14.645] [stderrLog] [info] Loading Transcript Info 
[2018-10-23 20:11:14.975] [stderrLog] [info] Loading Rank-Select Bit Array
[2018-10-23 20:11:15.031] [stderrLog] [info] There were 199,612 set bits in the bit array
[2018-10-23 20:11:15.042] [stderrLog] [info] Computing transcript lengths
[2018-10-23 20:11:15.042] [stderrLog] [info] Waiting to finish loading hash
[2018-10-23 20:11:20.618] [stderrLog] [info] Done loading index
[2018-10-23 20:11:20.618] [jointLog] [info] done
[2018-10-23 20:11:20.618] [jointLog] [info] Index contained 199,612 targets

Segmentation fault: 11

Desktop (please complete the following information):

• OS: [e.g. Ubuntu Linux, OSX] OSX
• Version [ If you are on OSX, the output of sw_vers. If you are on linux the output of uname -a and lsb_release -a]

ProductName: Mac OS X ProductVersion: 10.11.3 BuildVersion: 15D21

Additional context Add any other context about the problem here.

[rob-p]

Thanks for reporting this. It seems there is an osx bioconda issue (likely related to their massive backend upgrade). Hopefully we can fix this upstream in the next release. I. The meantime, can you see if this OSX binary works for you?

[dougbarrows]

Thank you! After unzipping and putting in my path and trying to run “salmon –version” I get the following error:

dyld: lazy symbol binding failed: Symbol not found: _os_unfair_lock_lock

Referenced from: /Users/douglasbarrows/Tools/salmon_0.11.4-pre_OSX/bin/./salmon (which was built for Mac OS X 10.13)

Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _os_unfair_lock_lock

Referenced from: /Users/douglasbarrows/Tools/salmon_0.11.4-pre_OSX/bin/./salmon (which was built for Mac OS X 10.13)

Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap: 5

Is that something you have seen before?

From: Rob Patro notifications@github.com Reply-To: COMBINE-lab/salmon reply@reply.github.com Date: Tuesday, October 23, 2018 at 8:25 PM To: COMBINE-lab/salmon salmon@noreply.github.com Cc: dougbarrows dbarrows@mail.rockefeller.edu, Author author@noreply.github.com Subject: Re: [COMBINE-lab/salmon] Segmentation fault 11 with bioconda build (#303)

Thanks for reporting this. It seems there is an osx bioconda issue (likely related to their massive backend upgrade). Hopefully we can fix this upstream in the next release. I. The meantime, can you see if thishttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_COMBINE-2Dlab_salmon_files_2383948_salmon-5F0.11.4-2Dpre-5FOSX.tar.gz&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=AcsC5BcigO3PFsA0uPOPf6vTyS2zaocuu4GaWSrIemY&m=wLNfpc7aJ_B1oE6XAqYsYKk5m7_TsLrkikeQql9eerg&s=40WTo4E4Odm5ZPLtYzGnDNBOb05l6L5woT7ke2vQ1L4&e= OSX binary works for you?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_COMBINE-2Dlab_salmon_issues_303-23issuecomment-2D432468434&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=AcsC5BcigO3PFsA0uPOPf6vTyS2zaocuu4GaWSrIemY&m=wLNfpc7aJ_B1oE6XAqYsYKk5m7_TsLrkikeQql9eerg&s=2d8a8eiQ0LuIlgyxoiTnsiwesaQ16X9sju0l7tT1WAw&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AYXm7zC7E77igQqcLnRZ1ABIhoVmQ9nuks5un7NtgaJpZM4X25Zf&d=DwMFaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=AcsC5BcigO3PFsA0uPOPf6vTyS2zaocuu4GaWSrIemY&m=wLNfpc7aJ_B1oE6XAqYsYKk5m7_TsLrkikeQql9eerg&s=fDJ8gfI64Ylwh4ObqOXFd-nHnxO4nOj0Hafu1HO8uNU&e=.

[rob-p]

Hrmm, that's a missing / different system library. Do the instructions here help at all?

[dougbarrows]

I still had the same error on that computer after following the instructions on the other thread. However, that computer is a bit older (OS 10.11.3), and when I used that OSX binary on my newer computer in lab (OS 10.13.4) it is working perfectly well so far. Thank you!

[rob-p]

Hi @dougbarrows --- just wanted to inform you that v0.12.0 has been released and is now also available via bioconda for both linux and osx. The osx segfault issue has been resolved.