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CahanLab / CellNet

CellNet: network biology applied to stem cell engineering
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cn_salmon Error: cannot open compressed file 'geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R' #10

Open Liang0328 opened 5 years ago

Liang0328 commented 5 years ago

Thank you for developing CellNet. I am trying to apply CellNet to some of my RNAseq data following your Nature Protocol paper. And the R file named 'geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R' is needed for parameter geneTabfname. But I can't find where to download it or don't know how to generate it. Could you tell me how to get the file?

pcahan1 commented 5 years ago

Hi,

Thanks for the interest in CellNet. _geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_042015.R' is bundled as part of the index (e.g. salmon.index.mouse.052617.tgz) that is used in the pre-processing steps. Please let us know whether this addresses the problem.

Liang0328 commented 5 years ago

Sorry, I still can't find 'geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R' in salmon.index.human.052617.tgz which I uncompressed. The compressed file contains the following content: hash.bin header.json indexing.log quasi_index.log refInfo.json rsd.bin sa.bin txpInfo.bin versionInfo.json And I noticed that versionInfo.json mentioned { "ReferenceFiles": [ "/media/ephemeral0/Homo_sapiens.GRCh38.cdna.ncrna.exo.Jul_05_2015.fa.gz" ] } Does it mean I need to download the fa.gz file?

I locally ran CellNet in my lab's cluster, error occured as followed: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'ref//geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R', probable reason 'No such file or directory'

Besides, I noticed the mapping rate=0%, detailed information exported by salmon as followed:

[2019-04-05 11:32:51.576] [jointLog] [info] Computed 0 rich equivalence classes for further processing [2019-04-05 11:32:51.576] [jointLog] [info] Counted 0 total reads in the equivalence classes [2019-04-05 11:33:01.673] [jointLog] [warning] Only 0 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-04-05 11:33:01.673] [jointLog] [info] Mapping rate = 0% [2019-04-05 11:33:01.673] [jointLog] [info] finished quantifyLibrary() [2019-04-05 11:33:01.673] [jointLog] [info] Starting optimizer [2019-04-05 11:33:01.705] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-04-05 11:33:01.706] [jointLog] [info] iteration = 0 | max rel diff. = -1.79769e+308 [2019-04-05 11:33:01.724] [jointLog] [info] iteration = 50 | max rel diff. = -1.79769e+308 [2019-04-05 11:33:01.734] [jointLog] [info] Finished optimizer [2019-04-05 11:33:01.734] [jointLog] [info] writing output

Wish I had clarified my problem for you.

lixin4306ren commented 3 years ago

@Liang0328 Got same issue. Did you solve this problem?

pcahan1 commented 3 years ago

We have now created a web application that takes as input an expression matrix (counts, TPM, or FPKM), and sample meta-data, and performs CellNet analysis. Additionally, this tool includes analysis of many state-of-the-art differentiation protocols, so that you can benchmark your results against those commonly used methods:

https://cahanlab.org/resources/agnosticCellNet_web/

starrzy commented 2 years ago

I got same error. Was the problem solved?