Hi,
I could successfully run the first part of GASV using the following syntax:
java -Xms20000m -Xmx20000m -jar BAMToGASV.jar /media/Illumina/Illumina/Thyroid-Cancer/Dr-Fouzan/Fowzan_R12.sorted.bam -OUTPUT_PREFIX /home/taha/Desktop/Report/GASV_result
But when I give the second command,
java -jar GASV.jar --batch /home/taha/Desktop/Report/GASV_result.gasv.in
I get the following error:
Warning: File: /home/taha/Desktop/Report/GASV_result_all.divergent contains a PR with overlapping reads GASV ignores such cases. The first such PR case encountered: HWI-ST409:90
0EMLACXX:7:1303:15930:3799 1 128611128710 - 1 128615 128714 +
Warning: File: /home/taha/Desktop/Report/GASV_result_all.inversion contains a PR with overlapping reads GASV ignores such cases. The first such PR case encountered: HWI-ST409:900EMLACXX:7:2302:4017:98476 1 569901570000 - 1 569906 569940 -
ERROR: Lmin has been increased beyond >= Lmax for ESP: HWI-ST409:900EMLACXX:7:2107:5570:140859 so halting program!
Can anybody throw some light?
I could successfully run the first part of GASV using the following syntax:
java -Xms20000m -Xmx20000m -jar BAMToGASV.jar /media/Illumina/Illumina/Thyroid-Cancer/Dr-Fouzan/Fowzan_R12.sorted.bam -OUTPUT_PREFIX /home/taha/Desktop/Report/GASV_result
But when I give the second command,
java -jar GASV.jar --batch /home/taha/Desktop/Report/GASV_result.gasv.in
I get the following error:
Warning: File: /home/taha/Desktop/Report/GASV_result_all.divergent contains a PR with overlapping reads GASV ignores such cases. The first such PR case encountered: HWI-ST409:90
0EMLACXX:7:1303:15930:3799 1 128611128710 - 1 128615 128714 +Warning: File: /home/taha/Desktop/Report/GASV_result_all.inversion contains a PR with overlapping reads GASV ignores such cases. The first such PR case encountered: HWI-ST409:90
0EMLACXX:7:2302:4017:98476 1 569901570000 - 1 569906 569940 -ERROR: Lmin has been increased beyond >= Lmax for ESP: HWI-ST409:90
0EMLACXX:7:2107:5570:140859 so halting program!Can anybody throw some light?