Abyss-pe error at the final stage

Question

[malabady]

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

[Damian Kao]

The read names of the pair are not matching according to Abyss.

[malabady]

I checked all files and they do match! something else is wrong.

[Damian Kao]

Actually its looking like the abyss-map command is formed wrong. What was the exact command you used to run abyss?

[malabady]

here is the command:

time /usr/local/abyss/latest/bin/abyss-pe np=10 k=64 name=Ab10_10 -d \
            lib='pe150_1 pe150_2 pe150_3' \
            mp='mp6k75 mp9k75 mpUnde75 mp6k150 mp9k150 mpUnde150' \
            pe150_1='P_R2_001_val_2.fq.gz P_R1_001_val_1.fq.gz' \
            pe150_2='D_R1_001_val_1.fq.gz D_R2_001_val_2.fq.gz' \
            pe150_3='K_R1_001_val_1.fq.gz K_R2_001_val_2.fq.gz' \
            mp6k75='mp6k_R1.mp.fastq.gz mp6k_R2.mp.fastq.gz' \
            mp9k75='mp9k_R1.mp.fastq.gz mp9k_R2.mp.fastq.gz' \
            mpUnde75='mpUndetermined_R1.mp.fastq.gz mpUndetermined_R2.mp.fastq.gz' \
            mp6k150='mp6k150_R1.mp.fastq.gz mp6k150_R2.mp.fastq.gz' \
            mp9k150='mp9k150_R1.mp.fastq.gz mp9k150_R2.mp.fastq.gz' \
            mpUnde150='mpUndetermined150_R1.mp.fastq.gz mpUndetermined150_R2.mp.fastq.gz' \
            se='mp6k_R1.unknown.fastq.gz mp6k_R2.unknown.fastq.gz mp6k.se.fastq.gz            mp9k_R1.unknown.fastq.gz mp9k_R2.unknown.fastq.gz mpUndetermined_R1.unknown.fastq.gz
            mpUndetermined_R2.unknown.fastq.gz mpUndetermined.se.fastq.gz All_R2_unpaired_2.fq.gz mp6k150_R1.unknown.fastq.gz mp6k150_R2.unknown.fastq.gz mp6k150.se.fastq.gz
            mpUndetermined150_R1.unknown.fastq.gz mp9k.se.fastq.gz All_R1_unpaired_1.fq.gz mpUndetermined150_R2.unknown.fastq.gz mpUndetermined150.se.fastq.gz'

[Damian Kao]

Try running your command with the --dry-run flag and then output to a text file. Can you copy the text file here?

[malabady]

already did that! and here is the it:

[Damian Kao]

Weird. That abyss-map command seems aright. If you just run that first abyss-map command by itself, does it work?

[malabady]

Yes,. abyss-map command is working fine when I run it by itself.

Answer 1

[malabady]

This error seems to be a glitch in abyss v.1.3.6. When I used the latest abyss version (1.9.0), abyss-pe successfully submitted abyss-map jobs. So the solution to this problem is to use the latest version of abyss.