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Alevin Failed

Open SoberDog opened this issue 1 year ago • 10 comments

When I used the example data to test the program, I get an error

Error in file(con, "r") : cannot open the connection
Calls: readLines -> file
In addition: Warning message:
In file(con, "r") :
  cannot open file './/SCASA_My_Project_20221014093239/1ALIGN//Sample_01_S1_L001_alignout/alevin/bfh.txt': No such file or directory
Execution halted
Loading required package: iterators
Loading required package: parallel
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/storage/data/GYD/Softwares/scasa/Test_Dataset/SCASA_My_Project_20221014093239/2QUANT/Sample_01_S1_L001_quant/Sample_eqClass.RData', probable reason 'No such file or directory'
Execution halted
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file './/SCASA_My_Project_20221014093239/2QUANT//Sample_01_S1_L001_quant//scasa_isoform_expression.RData', probable reason 'No such file or directory'
Execution halted
Congratulations! Scasa single cell RNA-Seq transcript quantification has completed in 30 seconds!
All done!

Then, I found a alevin log file from the result directory, alevin.log The alevin.log is show in below

[2022-10-14 09:34:38.938] [alevinLog] [info] Found 76267 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)
[2022-10-14 09:34:38.972] [alevinLog] [info] Filled with 72304 txp to gene entries
[2022-10-14 09:34:38.972] [alevinLog] [error] ERROR: Can't find gene mapping for : NM_001384956 w/ index 56214
[2022-10-14 09:34:38.972] [alevinLog] [error] ERROR: Txp to Gene Map not found for 3963 transcripts. Exiting

Thank you for helping me solve this problem

SoberDog avatar Oct 14 '22 01:10 SoberDog