Hi Everyone,
I'm a high school student working over the summer and I need to set-up ViralFusionSeq. However, I'm not able to complete the test run because I'm running into some errors. I have all the third-party software and followed the instaltion steps in the manual but still am getting problems. This here is the error message:
Thread 1 terminated abnormally: main=HASH(0x7f0a6c232f90) at viral.fusion.pl line 621.
Use of uninitialized value $ReturnData[0] in join or string at viral.fusion.pl
line 624 (#1)
(W uninitialized) An undefined value was used as if it were already
defined. It was interpreted as a "" or a 0, but maybe it was a mistake.
To suppress this warning assign a defined value to your variables.
To help you figure out what was undefined, perl will try to tell you the
name of the variable (if any) that was undefined. In some cases it cannot
do this, so it also tells you what operation you used the undefined value
in. Note, however, that perl optimizes your program and the operation
displayed in the warning may not necessarily appear literally in your
program. For example, "that $foo" is usually optimized into "that "
. $foo, and the warning will refer to the concatenation (.) operator,
even though there is no . in your program.
Thread 2 terminated abnormally: main=HASH(0x7f0a64232f90) at viral.fusion.pl line 622.
Use of uninitialized value $ReturnData2[0] in join or string at viral.fusion.pl
line 627 (#1)
sh: 1: /home/Gerry/Desktop/tools/bwa-0.6.2: Permission denied
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Can't open vfs_dev.HKCI5a_gz.RPm.out for writing : Permission denied at
/home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237 (#2)
(S inplace) The implicit opening of a file through use of the <>
filehandle, either implicitly under the -n or -p command-line
switches, or explicitly, failed for the indicated reason. Usually this
is because you don't have read permission for a file which you named on
the command line.
Uncaught exception from user code:
Can't open vfs_dev.HKCI5a_gz.RPm.out for writing : Permission denied at /home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237.
at /home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237.
RPmethod::exec_RPmethod('vfs_dev', 'HKCI5a_gz', 'vfs_dev.HKCI5a_gz.RPm.out', 24, 'CL7R_1_VFS.dynamic.min35.fq.gz', 'CL7R_2_VFS.dynamic.min35.fq.gz', '/home/jbs/Desktop/tools/vfs/references/human/hs37d5.fa', '/home/jbs/Desktop/tools/vfs/references/viral/hbv4.fa', '/home/jbs/Desktop/tools/bwa-0.6.2', ...) called at viral.fusion.pl line 668
I would appreciate any help on this.
Thanks
I'm a high school student working over the summer and I need to set-up ViralFusionSeq. However, I'm not able to complete the test run because I'm running into some errors. I have all the third-party software and followed the instaltion steps in the manual but still am getting problems. This here is the error message:
Thread 1 terminated abnormally: main=HASH(0x7f0a6c232f90) at viral.fusion.pl line 621.
Use of uninitialized value $ReturnData[0] in join or string at viral.fusion.pl
line 624 (#1)
(W uninitialized) An undefined value was used as if it were already
defined. It was interpreted as a "" or a 0, but maybe it was a mistake.
To suppress this warning assign a defined value to your variables.
To help you figure out what was undefined, perl will try to tell you the
name of the variable (if any) that was undefined. In some cases it cannot
do this, so it also tells you what operation you used the undefined value
in. Note, however, that perl optimizes your program and the operation
displayed in the warning may not necessarily appear literally in your
program. For example, "that $foo" is usually optimized into "that "
. $foo, and the warning will refer to the concatenation (.) operator,
even though there is no . in your program.
Thread 2 terminated abnormally: main=HASH(0x7f0a64232f90) at viral.fusion.pl line 622.
Use of uninitialized value $ReturnData2[0] in join or string at viral.fusion.pl
line 627 (#1)
sh: 1: /home/Gerry/Desktop/tools/bwa-0.6.2: Permission denied
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Can't open vfs_dev.HKCI5a_gz.RPm.out for writing : Permission denied at
/home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237 (#2)
(S inplace) The implicit opening of a file through use of the <>
filehandle, either implicitly under the -n or -p command-line
switches, or explicitly, failed for the indicated reason. Usually this
is because you don't have read permission for a file which you named on
the command line.
Uncaught exception from user code:
Can't open vfs_dev.HKCI5a_gz.RPm.out for writing : Permission denied at /home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237.
at /home/Gerry/Desktop/tools/vfs/include/RPmethod.pm line 237.
RPmethod::exec_RPmethod('vfs_dev', 'HKCI5a_gz', 'vfs_dev.HKCI5a_gz.RPm.out', 24, 'CL7R_1_VFS.dynamic.min35.fq.gz', 'CL7R_2_VFS.dynamic.min35.fq.gz', '/home/jbs/Desktop/tools/vfs/references/human/hs37d5.fa', '/home/jbs/Desktop/tools/vfs/references/viral/hbv4.fa', '/home/jbs/Desktop/tools/bwa-0.6.2', ...) called at viral.fusion.pl line 668
I would appreciate any help on this.
Thanks
Comment