Closed arthuryxt closed 5 years ago
Hi,
Please check the followings:
Thanks,
tw
Dear tw,
Thanks a lot for your time and effort 👍
./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
@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
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
Hi,
Do you have the novoalign license file? Is it in the same folder with novoalign?
Thanks,
tw
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
I guess this issue was due to the "array overflow" problem in JSFilter. (988c638826fcb9764664c89b88b8627c76de1e0c)
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:
The input file "run2_NCLscan_PE.main.JS2.sam" exists and is valid though.
Thanks for your help.