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TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
MIT License
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JSFilter Segmentation fault #7

Closed arthuryxt closed 5 years ago

arthuryxt commented 8 years ago

Hi,

I am trying to run v1.6 and the first three steps ran smoothly, but I cannot make it through JSFilter. Could you please kindly check on that? Below are the prompt messages:

cat: write error: Broken pipe
sh: line 1: 55989 Done(1)                 cat .//run2_NCLscan_PE.main.JS2.sam
     55990 Segmentation fault      | /project/NCLscan_master/bin/JSFilter 10 10 .//all.run2_NCLscan_PE.1.result > .//all.run2_NCLscan_PE.1.sam

The input file "run2_NCLscan_PE.main.JS2.sam" exists and is valid though.

Thanks for your help.

chiangtw commented 8 years ago

Hi,

Please check the followings:

  1. check the program "JSFilter" if it could be ran successfully. (without any parameters, it should print out the help message.)
  2. check the file size of "run2_NCLscan_PE.main.JS2.sam".
  3. please provide the system information, such as the operating system, the memory size, ...

Thanks,

tw

arthuryxt commented 8 years ago

Dear tw,

Thanks a lot for your time and effort 👍

  1. JSFilter works find without parameters:
./JSFilter 

JSFilter [J. length] [A. length] [Result]

[J. length]        INTEGER     The valid length of cross-junction alignemnts.
[A. length]        INTEGER     The minimal length of alignemnts in both sides.
[Result]           STRING      The file name that reporting results.

Example: (for all)
cat all.A.sam | ./JSFilter 10 50 A.result > A.filtered.sam 

Example: (for single data set)
cat a1.sam | ./JSFilter 10 10 a1.result > a1.filtered.sam
  1. the file "run2_NCLscan_PE.main.JS2.sam" is 372M, and below is the first a few lines:
@HD VN:1.0  SO:unsorted
@PG ID:novoalign    PN:novoalign    VN:V3.04.04 CL:novoalign -r A 1 -t 0,1 -d .//run2_NCLscan_PE.JS2.ndx -f .//run2_NCLscan_PE.main.unmapped_1.fastq .//run2_NCLscan_PE.main.unmapped_2.fastq --3Prime -o SAM
@SQ SN:Truseq_LPE_NM_021080.3_2580_478_202_1.0  LN:1000 AS:run2_NCLscan_PE.JS2.ndx
...
Truseq_2__4_1_2_4   83  Truseq_2__4_1_2_2.24    441 0   100M    =   441 100 CTACAGCTACTACCTGTACTACATGTATGCCAACATCATGGTGCTCAACAACCTCCGCAGTTCCTCAGTTTGAAACTACATGTAATTACGTAGAAGCTAC    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB    PG:Z:novoalign  AS:i:0  UQ:i:0  NM:i:0  MD:Z:100    PQ:i:4  SM:i:0  AM:i:0  ZS:Z:R  NH:i:16 HI:i:1  IH:i:1  Z3:i:540
  1. system info.
cpu    48x AMD Opteron 6176 SE
ram    129.1 GB
arch   x86_64 / 64-bit
glib  2.19
Linux kernel 3.10.29

Thanks, Arthur

chiangtw commented 8 years ago

Hi,

Do you have the novoalign license file? Is it in the same folder with novoalign?

Thanks,

tw

arthuryxt commented 8 years ago

Hi,

I do have a fresh two-month novoalign license file. It is in the same folder with novoalign. Without that, novoalign won't work with parameter "--3Prime".

Thanks, Arthur

chiangtw commented 5 years ago

I guess this issue was due to the "array overflow" problem in JSFilter. (988c638826fcb9764664c89b88b8627c76de1e0c)