Problems with Salmon Installation

[shaun webb]

Hi, I am trying out Salmon for the first time but I'm having some problems. It seems to have installed correctly but when I run `sudo make test` it fails tests 2 and 3 with the output below in the log file. Any ideas where to start looking for installation errors? If I try to run Salmon I just get the same response: salmon was invoked improperly.

Thanks for your help.

2/3 Testing: salmon_read_test_fmd

2/3 Test: salmon_read_test_fmd

Command: "/usr/bin/cmake" "-DTOPLEVEL_DIR=/homes/local/salmon/salmon" "-P" "/homes/local/salmon/salmon/cmake/TestSalmonFMD.cmake"

Directory: /homes/local/salmon/salmon/src

"salmon_read_test_fmd" start time: Mar 16 12:14 GMT

Output:

----------------------------------------------------------

sample_data/

sample_data/transcripts.fasta

sample_data/reads_1.fastq

sample_data/reads_2.fastq

Version Info: This is the most recent version of Salmon.

/homes/local/salmon/salmon/src/salmon was invoked improperly.

For usage information, try /homes/local/salmon/salmon/src/salmon --help

Exiting.

Version Info: This is the most recent version of Salmon.

/homes/local/salmon/salmon/src/salmon was invoked improperly.

For usage information, try /homes/local/salmon/salmon/src/salmon --help

Exiting.

CMake Error at /homes/local/salmon/salmon/cmake/TestSalmonFMD.cmake:32 (message):

  Salmon (read --- fmd-index) failed to produce output

<end of output>

Test time =   0.32 sec

----------------------------------------------------------

Test Failed.

"salmon_read_test_fmd" end time: Mar 16 12:14 GMT

"salmon_read_test_fmd" time elapsed: 00:00:00

----------------------------------------------------------

[Rob]

Hi Shaun,

  One place to look would be the ctest output logs.  In the directory where you built salmon, they should be under the subdirectory `Testing/Temporary/`.  They will list the actual output, if any, of the tests.  From the message you're getting, it looks like a possible permission error where it is attempting to write the output files.  Perhaps the index wasn't generated and hence the test quantification can't be performed.  What happens when you cd into a directory where you have permission and run:

$ salmon index -t <SALMON_SOURCE_DIR>/sample_data/transcripts.fasta -i test_index

[shaun webb]

I still get the same message. The log I pasted above is from the Testing/Temporary/LastTest.log file.

The output for CTestCostData.txt is :

unit_tests 2 33.4527

salmon_read_test_fmd 0 0

salmon_read_test_quasi 0 0

---

salmon_read_test_fmd

salmon_read_test_quasi

[Rob]

Hrmm, out of curiosity, can you run the compiled (but not yet installed) binary?  If you're in <SALMON_SOURCE_DIR>/build, and you run:

$ ./src/salmon --help

what do you see?  How about:

$ ./src/salmon index -t ../sample_data/transcripts.fasta -i test_index 

I'm curious whether the problem is the binary, or the manner in which it was installed.

[shaun webb]

So I have reinstalled using the precompiled binary and it seems to be working fine. Thanks for your help!

[Rob]

Hi Shaun,

  I'm glad to hear the pre-compiled binary is working for you; sorry for the difficulty with the install.  I haven't seen that issue before, but if it pops up again, I'll be happy to dig into it a little deeper.

Best,

Rob

[Petros Tsantoulis]

Hello,

I'm getting a similar error compiling from source on a specific machine, but not on another one. Specifically, make test fails at the 2nd and 3rd test.
Specifically:
tsantou@sib-pc11:/export/big2/ptsant/NGS/downloads/salmon/build$ salmon

Version Info: This is the most recent version of Salmon.

salmon was invoked improperly.
For usage information, try salmon --help
Exiting.
ptsantou@sib-pc11:/export/big2/ptsant/NGS/downloads/salmon/build$ make test
Running tests...
/usr/bin/ctest --force-new-ctest-process
Test project /export/big2/ptsant/NGS/downloads/salmon/build
    Start 1: unit_tests
1/3 Test #1: unit_tests .......................   Passed   23.66 sec
    Start 2: salmon_read_test_fmd
2/3 Test #2: salmon_read_test_fmd .............***Failed    0.63 sec
    Start 3: salmon_read_test_quasi
3/3 Test #3: salmon_read_test_quasi ...........***Failed    0.09 sec

33% tests passed, 2 tests failed out of 3

Total Test time (real) =  24.42 sec

The following tests FAILED:
      2 - salmon_read_test_fmd (Failed)
      3 - salmon_read_test_quasi (Failed)
Errors while running CTest
make: *** [test] Error 8

Note that when I try to build the index I get this:
tsantou@sib-pc11:/export/big2/ptsant/NGS/reference/salmon$ salmon index -i gencode.v24 -t ../gencode.v24/gencode.v24.pc_translations.fa.gz

Version Info: This is the most recent version of Salmon.

index ["gencode.v24"] did not previously exist  . . . creating it
[2016-04-26 16:34:51.558] [jLog] [info] building index
RapMap Indexer
Exception : [Unsupported format]
salmon index was invoked improperly.
For usage information, try salmon index --help
Exiting.

Any ideas?

Thanks a lot!
Petros

[Rob Patro]

Hi Petros,

  The Fastq reader we use (from Jellyfish) doesn't support gz files natively.  Does the following work?

tsantou@sib-pc11:/export/big2/ptsant/NGS/reference/salmon$ salmon index -i gencode.v24 -t <( gunzip -c ../gencode.v24/gencode.v24.pc_translations.fa.gz)

That will decompress the gzipped file on the fly.  The issue with the test may be related to not running make install before running make test (I have a fix for that, but it's not in master yet).  Let me know if either of these help.

Best,

Rob

Sent from Rob's iPhone.  Please excuse the brevity and any typos.

--
Sailfish is available at https://github.com/kingsfordgroup/sailfish
Citation:
Patro, Rob, Stephen M. Mount, and Carl Kingsford. "Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms." Nature biotechnology 32.5 (2014): 462-464.
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[Petros Tsantoulis]

Hello Rob,

Thanks a lot for your reply. I have succesfully used Salmon on one machine and am happy with the results. However, the other machine, on which compilation seems to be OK, fails with the message I showed previously.

When I use a quant command:

$ salmon quant -p 5 --libType SF --index ../../reference/salmon/gencode.v24 -r <(gzip -dc 361174.fastq.gz) -o 361174.salmon

Version Info: This is the most recent version of Salmon.

# salmon (mapping-based) v0.6.0
# [ program ] => salmon
# [ command ] => quant
# [ threads ] => { 5 }
# [ libType ] => { FS }
# [ index ] => { ../../reference/salmon/gencode.v24 }
# [ unmatedReads ] => { /dev/fd/63 }
# [ output ] => { 361174.salmon }
Exception : [locale::facet::_S_create_c_locale name not valid]
salmon quant was invoked improperly.
For usage information, try salmon quant --help
Exiting.


Index building seems successful and make also seems to work. The Debian binary works fine, too, and is what I installed in this particular machine.

In the end, I don't want to waste your time, I was just a bit curious as to why it failed to build on one machine.

Best,
Petros

[Napoleon Little]

Hi, I have another problem different from you when I install salmon on my ubuntu computer.When I made test, only 67% tests passed, the test 1 unit_tests failed. Could
you tell me what kinds of error happened in my salmon installation?

在 2016年3月16日星期三 UTC+8下午11:04:47，shaun webb写道：

[Rob]

Hi Napoleon,

  Could you post the output of the testing log?  In the directory where the test were run (likely in the build directory), there should be a folder Testing/Temporary, that contains a file "LastTestFailed.log".  This file should contain more details about exactly what tests failed.  Could you post that information here?  It's hard to say what might have gone wrong without this information.

--Rob

[Napoleon Little]

Hi Rob,

   after several days, I make test again, but this time I got test 1 and test failed! the lasttest.log is as follows,

Start testing: Jan 10 13:54 CST
----------------------------------------------------------
1/3 Testing: unit_tests
1/3 Test: unit_tests
Command: "/usr/bin/cmake" "-DTOPLEVEL_DIR=/usr/local" "-P" "/home/you/文档/salmon-master/cmake/UnitTests.cmake"
Directory: /home/you/文档/salmon-master/build/src
"unit_tests" start time: Jan 10 13:54 CST
Output:
----------------------------------------------------------
CMake Error at /home/you/文档/salmon-master/cmake/UnitTests.cmake:7 (message):
  Error running No such file or directory


<end of output>
Test time =   0.01 sec
----------------------------------------------------------
Test Failed.
"unit_tests" end time: Jan 10 13:54 CST
"unit_tests" time elapsed: 00:00:00
----------------------------------------------------------

2/3 Testing: salmon_read_test_fmd
2/3 Test: salmon_read_test_fmd

Command: "/usr/bin/cmake" "-DTOPLEVEL_DIR=/home/you/文档/salmon-master" "-P" "/home/you/文档/salmon-master/cmake/TestSalmonFMD.cmake"
Directory: /home/you/文档/salmon-master/build/src
"salmon_read_test_fmd" start time: Jan 10 13:54 CST
Output:
----------------------------------------------------------
sample_data/
sample_data/transcripts.fasta
tar: sample_data/transcripts.fasta：无法 open: 文件已存在
sample_data/reads_1.fastq
sample_data/reads_2.fastq
tar: sample_data/reads_1.fastq：无法 open: 文件已存在
tar: sample_data/reads_2.fastq：无法 open: 文件已存在
tar: sample_data：无法 utime: 不允许的操作
tar: 由于前次错误，将以上次的错误状态退出
CMake Error at /home/you/文档/salmon-master/cmake/TestSalmonFMD.cmake:7 (message):
  Error untarring sample_data.tgz


<end of output>
Test time =   0.03 sec
----------------------------------------------------------
Test Failed.
"salmon_read_test_fmd" end time: Jan 10 13:54 CST

"salmon_read_test_fmd" time elapsed: 00:00:00
----------------------------------------------------------

3/3 Testing: salmon_read_test_quasi
3/3 Test: salmon_read_test_quasi
Command: "/usr/bin/cmake" "-DTOPLEVEL_DIR=/home/you/文档/salmon-master" "-P" "/home/you/文档/salmon-master/cmake/TestSalmonQuasi.cmake"
Directory: /home/you/文档/salmon-master/build/src
"salmon_read_test_quasi" start time: Jan 10 13:54 CST
Output:
----------------------------------------------------------

Version Info: This is the most recent version of Salmon.

[2017-01-10 13:54:09.203] [jLog] [info] building index
RapMap Indexer

[Step 1 of 4] : counting k-mers
Elapsed time: 0.00051845s

Replaced 0 non-ATCG nucleotides
Clipped poly-A tails from 0 transcripts
Building rank-select dictionary and saving to disk done
Elapsed time: 8.344e-06s
Writing sequence data to file . . . done
Elapsed time: 4.9329e-05s
[info] Building 32-bit suffix array (length of generalized text is 28577)
Building suffix array . . . success
saving to disk . . . done
Elapsed time: 0.00015503s
done
Elapsed time: 0.00582574s
  processed 0 positions
khash had 18901 keys
saving hash to disk . . . done
Elapsed time: 0.00203268s
[2017-01-10 13:54:09.230] [jLog] [info] done building index

Version Info: This is the most recent version of Salmon.

### salmon (mapping-based) v0.7.2
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { sample_salmon_quasi_index }
### [ libType ] => { IU }
### [ mates1 ] => { reads_1.fastq }
### [ mates2 ] => { reads_2.fastq }
### [ output ] => { sample_salmon_quasi_quant }
Logs will be written to sample_salmon_quasi_quant/logs
[1m[2017-01-10 13:54:09.585] [jointLog] [info] parsing read library format
[00m [1m[2017-01-10 13:54:09.585] [jointLog] [info] There is 1 library.
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] Loading Suffix Array 
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] Loading Transcript Info 
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] Loading Rank-Select Bit Array
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] There were 15 set bits in the bit array
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] Computing transcript lengths
[00m [1m[2017-01-10 13:54:09.613] [stderrLog] [info] Waiting to finish loading hash
[00m [1m[2017-01-10 13:54:09.614] [stderrLog] [info] Successfully loaded position hash
[00m [1m[2017-01-10 13:54:09.615] [stderrLog] [info] Done loading index
[00m [1m[2017-01-10 13:54:09.613] [jointLog] [info] Loading Quasi index
[00m [1m[2017-01-10 13:54:09.613] [jointLog] [info] Loading 32-bit quasi index
[00m [1m[2017-01-10 13:54:09.615] [jointLog] [info] done
[00m [1m[2017-01-10 13:54:09.615] [jointLog] [info] Index contained 15 targets
[00m


[1m[2017-01-10 13:54:09.811] [jointLog] [info] Computed 21 rich equivalence classes for further processing
[00m [1m[2017-01-10 13:54:09.811] [jointLog] [info] Counted 10000 total reads in the equivalence classes 
[00m [33m [1m[2017-01-10 13:54:09.814] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[00m [1m[2017-01-10 13:54:09.814] [jointLog] [info] Mapping rate = 100%

[00m [1m[2017-01-10 13:54:09.814] [jointLog] [info] finished quantifyLibrary()
[00m [1m[2017-01-10 13:54:09.814] [jointLog] [info] Starting optimizer
[00m [1m[2017-01-10 13:54:09.815] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[00m [1m[2017-01-10 13:54:09.815] [jointLog] [info] iteration = 0 | max rel diff. = 9.75595
[00m [1m[2017-01-10 13:54:09.815] [jointLog] [info] iteration = 100 | max rel diff. = 4.28611e-05
[00m [1m[2017-01-10 13:54:09.815] [jointLog] [info] Finished optimizer
[00m [1m[2017-01-10 13:54:09.815] [jointLog] [info] writing output 

[00mSalmon (read) ran successfully
<end of output>
Test time =   1.78 sec
----------------------------------------------------------
Test Passed.
"salmon_read_test_quasi" end time: Jan 10 13:54 CST
"salmon_read_test_quasi" time elapsed: 00:00:01
----------------------------------------------------------

End testing: Jan 10 13:54 CST

在 2017年1月3日星期二 UTC+8下午10:19:02，Rob写道：