Entering edit mode
8.9 years ago
malabady
▴
30
Hi,
I getting the following error. When I looked at my fastq files, I found that reads in R1 and R2 files are in the same order. What is the cause of this error and how to fix it? Thanks a lot.
abyss-map: invalid option -- l
abyss-map: invalid option -- 6
abyss-map: invalid option -- 4
Try `abyss-map --help' for more information.
Mateless 0
Unaligned 0
Singleton 0
FR 0
RF 0
FF 0
Different 0
Total 0
abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match.
error: `pe150_1-3.hist': No such file or directory
make: *** [pe150_1-3.dist] Error 1
make: *** Deleting file `pe150_1-3.dist'
real 0m1.379s
user 0m0.015s
sys 0m0.082s
The read names of the pair are not matching according to Abyss.
I checked all files and they do match! something else is wrong.
Actually its looking like the abyss-map command is formed wrong. What was the exact command you used to run abyss?
here is the command:
Try running your command with the
--dry-run
flag and then output to a text file. Can you copy the text file here?already did that! and here is the it:
Weird. That abyss-map command seems aright. If you just run that first abyss-map command by itself, does it work?
Yes,. abyss-map command is working fine when I run it by itself.