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:

	GNU Make 3.81
	Copyright (C) 2006 Free Software Foundation, Inc.
	This is free software; see the source for copying conditions.
	There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
	PARTICULAR PURPOSE.
	This program built for x86_64-redhat-linux-gnu
	Reading makefiles...
	Reading makefile `/usr/local/abyss/latest/bin/abyss-pe'...
	Updating makefiles....
	Considering target file `/usr/local/abyss/latest/bin/abyss-pe'.
	Looking for an implicit rule for `/usr/local/abyss/latest/bin/abyss-pe'.
	No implicit rule found for `/usr/local/abyss/latest/bin/abyss-pe'.
	Finished prerequisites of target file `/usr/local/abyss/latest/bin/abyss-pe'.
	No need to remake target `/usr/local/abyss/latest/bin/abyss-pe'.
	Updating goal targets....
	Considering target file `default'.
	File `default' does not exist.
	Considering target file `unitigs'.
	File `unitigs' does not exist.
	Considering target file `Ab10_10-unitigs.fa'.
	Looking for an implicit rule for `Ab10_10-unitigs.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Found an implicit rule for `Ab10_10-unitigs.fa'.
	Considering target file `Ab10_10-3.fa'.
	Looking for an implicit rule for `Ab10_10-3.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-1.fa'.
	Trying implicit prerequisite `Ab10_10-2.adj'.
	Trying implicit prerequisite `Ab10_10-2.path'.
	Found an implicit rule for `Ab10_10-3.fa'.
	Considering target file `Ab10_10-1.fa'.
	Looking for an implicit rule for `Ab10_10-1.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Found an implicit rule for `Ab10_10-1.fa'.
	Finished prerequisites of target file `Ab10_10-1.fa'.
	No need to remake target `Ab10_10-1.fa'.
	Considering target file `Ab10_10-2.adj'.
	Looking for an implicit rule for `Ab10_10-2.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-1.adj'.
	Found an implicit rule for `Ab10_10-2.adj'.
	Considering target file `Ab10_10-1.adj'.
	Looking for an implicit rule for `Ab10_10-1.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-1.fa'.
	Found an implicit rule for `Ab10_10-1.adj'.
	Pruning file `Ab10_10-1.fa'.
	Finished prerequisites of target file `Ab10_10-1.adj'.
	Prerequisite `Ab10_10-1.fa' is older than target `Ab10_10-1.adj'.
	No need to remake target `Ab10_10-1.adj'.
	Finished prerequisites of target file `Ab10_10-2.adj'.
	Prerequisite `Ab10_10-1.adj' is older than target `Ab10_10-2.adj'.
	No need to remake target `Ab10_10-2.adj'.
	Considering target file `Ab10_10-2.path'.
	Looking for an implicit rule for `Ab10_10-2.path'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-1.fa'.
	Trying implicit prerequisite `Ab10_10-2.adj'.
	Found an implicit rule for `Ab10_10-2.path'.
	Pruning file `Ab10_10-1.fa'.
	Pruning file `Ab10_10-2.adj'.
	Finished prerequisites of target file `Ab10_10-2.path'.
	Prerequisite `Ab10_10-1.fa' is older than target `Ab10_10-2.path'.
	Prerequisite `Ab10_10-2.adj' is older than target `Ab10_10-2.path'.
	No need to remake target `Ab10_10-2.path'.
	Finished prerequisites of target file `Ab10_10-3.fa'.
	Prerequisite `Ab10_10-1.fa' is older than target `Ab10_10-3.fa'.
	Prerequisite `Ab10_10-2.adj' is older than target `Ab10_10-3.fa'.
	Prerequisite `Ab10_10-2.path' is older than target `Ab10_10-3.fa'.
	No need to remake target `Ab10_10-3.fa'.
	Finished prerequisites of target file `Ab10_10-unitigs.fa'.
	Prerequisite `Ab10_10-3.fa' is older than target `Ab10_10-unitigs.fa'.
	No need to remake target `Ab10_10-unitigs.fa'.
	Finished prerequisites of target file `unitigs'.
	Must remake target `unitigs'.
	Successfully remade target file `unitigs'.
	Considering target file `contigs'.
	File `contigs' does not exist.
	Looking for an implicit rule for `Ab10_10-contigs.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Looking for a rule with intermediate file `Ab10_10-6.fa'.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-4.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-4.fa'.
	Looking for a rule with intermediate file `Ab10_10-4.fa'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-3.adj'.
	Trying implicit prerequisite `Ab10_10-3.dist'.
	Trying implicit prerequisite `Ab10_10-5.fa'.
	Looking for a rule with intermediate file `Ab10_10-5.fa'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-4.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-4.fa'.
	Looking for a rule with intermediate file `Ab10_10-4.fa'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-3.adj'.
	Trying implicit prerequisite `Ab10_10-3.dist'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path3'.
	Looking for a rule with intermediate file `Ab10_10-4.path3'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path2'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path2'.
	Looking for a rule with intermediate file `Ab10_10-4.path2'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path1'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path1'.
	Looking for a rule with intermediate file `Ab10_10-4.path1'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-3.dist'.
	Trying implicit prerequisite `Ab10_10-5.adj'.
	Trying implicit prerequisite `Ab10_10-5.path'.
	Found an implicit rule for `Ab10_10-contigs.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Considering target file `Ab10_10-3.adj'.
	Looking for an implicit rule for `Ab10_10-3.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-1.fa'.
	Trying implicit prerequisite `Ab10_10-2.adj'.
	Found an implicit rule for `Ab10_10-3.adj'.
	Pruning file `Ab10_10-1.fa'.
	Pruning file `Ab10_10-2.adj'.
	Finished prerequisites of target file `Ab10_10-3.adj'.
	Prerequisite `Ab10_10-1.fa' is older than target `Ab10_10-3.adj'.
	Prerequisite `Ab10_10-2.adj' is older than target `Ab10_10-3.adj'.
	No need to remake target `Ab10_10-3.adj'.
	Pruning file `Ab10_10-3.fa'.
	Looking for an implicit rule for `pe150_1-3.dist'.
	Trying pattern rule with stem `pe150_1'.
	Trying implicit prerequisite `pe150_1-3.sam.gz'.
	Trying pattern rule with stem `pe150_1'.
	Trying implicit prerequisite `pe150_1-3.bam'.
	Trying pattern rule with stem `pe150_1'.
	Trying rule prerequisite `Ab10_10-3.fa'.
	Found an implicit rule for `pe150_1-3.dist'.
	Looking for an implicit rule for `pe150_2-3.dist'.
	Trying pattern rule with stem `pe150_2'.
	Trying implicit prerequisite `pe150_2-3.sam.gz'.
	Trying pattern rule with stem `pe150_2'.
	Trying implicit prerequisite `pe150_2-3.bam'.
	Trying pattern rule with stem `pe150_2'.
	Trying rule prerequisite `Ab10_10-3.fa'.
	Found an implicit rule for `pe150_2-3.dist'.
	Pruning file `Ab10_10-3.fa'.
	Looking for an implicit rule for `pe150_3-3.dist'.
	Trying pattern rule with stem `pe150_3'.
	Trying implicit prerequisite `pe150_3-3.sam.gz'.
	Trying pattern rule with stem `pe150_3'.
	Trying implicit prerequisite `pe150_3-3.bam'.
	Trying pattern rule with stem `pe150_3'.
	Trying rule prerequisite `Ab10_10-3.fa'.
	Found an implicit rule for `pe150_3-3.dist'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Considering target file `Ab10_10-4.adj'.
	File `Ab10_10-4.adj' does not exist.
	Looking for an implicit rule for `Ab10_10-4.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-3.adj'.
	Trying implicit prerequisite `Ab10_10-3.dist'.
	Found an implicit rule for `Ab10_10-4.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Considering target file `Ab10_10-3.dist'.
	File `Ab10_10-3.dist' does not exist.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Considering target file `pe150_1-3.dist'.
	Pruning file `Ab10_10-3.fa'.
	Finished prerequisites of target file `pe150_1-3.dist'.
	Prerequisite `Ab10_10-3.fa' is older than target `pe150_1-3.dist'.
	No need to remake target `pe150_1-3.dist'.
	Considering target file `pe150_2-3.dist'.
	File `pe150_2-3.dist' does not exist.
	Pruning file `Ab10_10-3.fa'.
	Finished prerequisites of target file `pe150_2-3.dist'.
	Must remake target `pe150_2-3.dist'.
	abyss-map -j10 -l64 D_R1_001_val_1.fq.gz D_R2_001_val_2.fq.gz Ab10_10-3.fa \
	|abyss-fixmate -l64 -h pe150_2-3.hist \
	|sort -snk3 -k4 \
	|DistanceEst -j10 -k64 -l64 -s200 -n10 -o pe150_2-3.dist pe150_2-3.hist
	Successfully remade target file `pe150_2-3.dist'.
	Considering target file `pe150_3-3.dist'.
	File `pe150_3-3.dist' does not exist.
	Pruning file `Ab10_10-3.fa'.
	Finished prerequisites of target file `pe150_3-3.dist'.
	Must remake target `pe150_3-3.dist'.
	abyss-map -j10 -l64 K_R1_001_val_1.fq.gz K_R2_001_val_2.fq.gz Ab10_10-3.fa \
	|abyss-fixmate -l64 -h pe150_3-3.hist \
	|sort -snk3 -k4 \
	|DistanceEst -j10 -k64 -l64 -s200 -n10 -o pe150_3-3.dist pe150_3-3.hist
	Successfully remade target file `pe150_3-3.dist'.
	Finished prerequisites of target file `Ab10_10-3.dist'.
	Must remake target `Ab10_10-3.dist'.
	abyss-todot --dist -e Ab10_10-3.fa pe150_1-3.dist pe150_2-3.dist pe150_3-3.dist >Ab10_10-3.dist
	Successfully remade target file `Ab10_10-3.dist'.
	Finished prerequisites of target file `Ab10_10-4.adj'.
	Must remake target `Ab10_10-4.adj'.
	Overlap -k64 -g Ab10_10-4.adj -o Ab10_10-4.fa Ab10_10-3.fa Ab10_10-3.adj Ab10_10-3.dist
	Successfully remade target file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Considering target file `Ab10_10-5.adj'.
	File `Ab10_10-5.adj' does not exist.
	Looking for an implicit rule for `Ab10_10-5.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-3.fa'.
	Trying implicit prerequisite `Ab10_10-4.fa'.
	Trying implicit prerequisite `Ab10_10-4.adj'.
	Trying implicit prerequisite `Ab10_10-4.path3'.
	Found an implicit rule for `Ab10_10-5.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Considering target file `Ab10_10-4.fa'.
	File `Ab10_10-4.fa' was considered already.
	Considering target file `Ab10_10-4.path3'.
	File `Ab10_10-4.path3' does not exist.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Considering target file `Ab10_10-4.path2'.
	File `Ab10_10-4.path2' does not exist.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-4.adj'.
	Considering target file `Ab10_10-4.path1'.
	File `Ab10_10-4.path1' does not exist.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-3.dist'.
	Finished prerequisites of target file `Ab10_10-4.path1'.
	Must remake target `Ab10_10-4.path1'.
	SimpleGraph -j10 -k64 -o Ab10_10-4.path1 Ab10_10-4.adj Ab10_10-3.dist
	Successfully remade target file `Ab10_10-4.path1'.
	Finished prerequisites of target file `Ab10_10-4.path2'.
	Must remake target `Ab10_10-4.path2'.
	MergePaths -j10 -k64 -o Ab10_10-4.path2 Ab10_10-4.adj Ab10_10-4.path1
	Successfully remade target file `Ab10_10-4.path2'.
	Finished prerequisites of target file `Ab10_10-4.path3'.
	Must remake target `Ab10_10-4.path3'.
	PathOverlap --assemble -k64 Ab10_10-4.adj Ab10_10-4.path2 >Ab10_10-4.path3
	Successfully remade target file `Ab10_10-4.path3'.
	Finished prerequisites of target file `Ab10_10-5.adj'.
	Must remake target `Ab10_10-5.adj'.
	cat Ab10_10-3.fa Ab10_10-4.fa \
	|PathConsensus -k64 -p0.9 -o Ab10_10-5.path -s Ab10_10-5.fa -g Ab10_10-5.adj - Ab10_10-4.adj Ab10_10-4.path3
	Successfully remade target file `Ab10_10-5.adj'.
	Considering target file `Ab10_10-5.path'.
	File `Ab10_10-5.path' was considered already.
	Considering target file `Ab10_10-contigs.fa'.
	File `Ab10_10-contigs.fa' does not exist.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-5.adj'.
	Pruning file `Ab10_10-5.path'.
	Considering target file `Ab10_10-6.fa'.
	File `Ab10_10-6.fa' does not exist.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.fa'.
	Pruning file `Ab10_10-3.adj'.
	Pruning file `Ab10_10-4.adj'.
	Pruning file `Ab10_10-5.adj'.
	Pruning file `Ab10_10-5.path'.
	Pruning file `Ab10_10-4.fa'.
	Considering target file `Ab10_10-5.fa'.
	File `Ab10_10-5.fa' was considered already.
	Finished prerequisites of target file `Ab10_10-6.fa'.
	Must remake target `Ab10_10-6.fa'.
	cat Ab10_10-3.fa Ab10_10-4.fa Ab10_10-5.fa |MergeContigs -k64 -o Ab10_10-6.fa - Ab10_10-5.adj Ab10_10-5.path
	Successfully remade target file `Ab10_10-6.fa'.
	Finished prerequisites of target file `Ab10_10-contigs.fa'.
	Must remake target `Ab10_10-contigs.fa'.
	ln -sf Ab10_10-6.fa Ab10_10-contigs.fa
	Successfully remade target file `Ab10_10-contigs.fa'.
	Finished prerequisites of target file `contigs'.
	Must remake target `contigs'.
	Successfully remade target file `contigs'.
	Considering target file `contigs-dot'.
	File `contigs-dot' does not exist.
	Looking for an implicit rule for `Ab10_10-contigs.dot'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.dot'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.dot'.
	Looking for a rule with intermediate file `Ab10_10-6.dot'.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-5.adj'.
	Trying implicit prerequisite `Ab10_10-5.path'.
	Found an implicit rule for `Ab10_10-contigs.dot'.
	Pruning file `Ab10_10-5.adj'.
	Pruning file `Ab10_10-5.path'.
	Considering target file `Ab10_10-contigs.dot'.
	File `Ab10_10-contigs.dot' does not exist.
	Pruning file `Ab10_10-5.adj'.
	Pruning file `Ab10_10-5.path'.
	Considering target file `Ab10_10-6.dot'.
	File `Ab10_10-6.dot' does not exist.
	Pruning file `Ab10_10-5.adj'.
	Pruning file `Ab10_10-5.path'.
	Finished prerequisites of target file `Ab10_10-6.dot'.
	Must remake target `Ab10_10-6.dot'.
	PathOverlap --overlap --dot -k64 Ab10_10-5.adj Ab10_10-5.path >Ab10_10-6.dot
	Successfully remade target file `Ab10_10-6.dot'.
	Finished prerequisites of target file `Ab10_10-contigs.dot'.
	Must remake target `Ab10_10-contigs.dot'.
	ln -sf Ab10_10-6.dot Ab10_10-contigs.dot
	Successfully remade target file `Ab10_10-contigs.dot'.
	Finished prerequisites of target file `contigs-dot'.
	Must remake target `contigs-dot'.
	Successfully remade target file `contigs-dot'.
	Considering target file `scaffolds'.
	File `scaffolds' does not exist.
	Looking for an implicit rule for `Ab10_10-scaffolds.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-8.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-8.fa'.
	Looking for a rule with intermediate file `Ab10_10-8.fa'.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-7.fa'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-7.fa'.
	Looking for a rule with intermediate file `Ab10_10-7.fa'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-6.dot'.
	Trying implicit prerequisite `Ab10_10-6.path'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-6.dot'.
	Trying implicit prerequisite `Ab10_10-6.path'.
	Looking for a rule with intermediate file `Ab10_10-6.path'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying rule prerequisite `Ab10_10-6.dot'.
	Trying rule prerequisite `mp6k75-6.dist.dot'.
	Trying pattern rule with stem `Ab10_10'.
	Trying rule prerequisite `Ab10_10-6.dot'.
	Trying rule prerequisite `mp6k75-6.dist.dot'.
	Looking for a rule with intermediate file `mp6k75-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mp6k75'.
	Trying implicit prerequisite `mp6k75-6.sam.gz'.
	Trying pattern rule with stem `mp6k75'.
	Trying implicit prerequisite `mp6k75-6.bam'.
	Trying pattern rule with stem `mp6k75'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying rule prerequisite `mp9k75-6.dist.dot'.
	Looking for a rule with intermediate file `mp9k75-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mp9k75'.
	Trying implicit prerequisite `mp9k75-6.sam.gz'.
	Trying pattern rule with stem `mp9k75'.
	Trying implicit prerequisite `mp9k75-6.bam'.
	Trying pattern rule with stem `mp9k75'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying rule prerequisite `mpUnde75-6.dist.dot'.
	Looking for a rule with intermediate file `mpUnde75-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mpUnde75'.
	Trying implicit prerequisite `mpUnde75-6.sam.gz'.
	Trying pattern rule with stem `mpUnde75'.
	Trying implicit prerequisite `mpUnde75-6.bam'.
	Trying pattern rule with stem `mpUnde75'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying rule prerequisite `mp6k150-6.dist.dot'.
	Looking for a rule with intermediate file `mp6k150-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mp6k150'.
	Trying implicit prerequisite `mp6k150-6.sam.gz'.
	Trying pattern rule with stem `mp6k150'.
	Trying implicit prerequisite `mp6k150-6.bam'.
	Trying pattern rule with stem `mp6k150'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying rule prerequisite `mp9k150-6.dist.dot'.
	Looking for a rule with intermediate file `mp9k150-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mp9k150'.
	Trying implicit prerequisite `mp9k150-6.sam.gz'.
	Trying pattern rule with stem `mp9k150'.
	Trying implicit prerequisite `mp9k150-6.bam'.
	Trying pattern rule with stem `mp9k150'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying rule prerequisite `mpUnde150-6.dist.dot'.
	Looking for a rule with intermediate file `mpUnde150-6.dist.dot'.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `mpUnde150'.
	Trying implicit prerequisite `mpUnde150-6.sam.gz'.
	Trying pattern rule with stem `mpUnde150'.
	Trying implicit prerequisite `mpUnde150-6.bam'.
	Trying pattern rule with stem `mpUnde150'.
	Trying rule prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-7.adj'.
	Trying implicit prerequisite `Ab10_10-7.path'.
	Found an implicit rule for `Ab10_10-scaffolds.fa'.
	Considering target file `Ab10_10-7.adj'.
	File `Ab10_10-7.adj' does not exist.
	Looking for an implicit rule for `Ab10_10-7.adj'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-6.fa'.
	Trying implicit prerequisite `Ab10_10-6.dot'.
	Trying implicit prerequisite `Ab10_10-6.path'.
	Found an implicit rule for `Ab10_10-7.adj'.
	Pruning file `Ab10_10-6.fa'.
	Pruning file `Ab10_10-6.dot'.
	Considering target file `Ab10_10-6.path'.
	File `Ab10_10-6.path' does not exist.
	Pruning file `Ab10_10-6.dot'.
	Considering target file `mp6k75-6.dist.dot'.
	File `mp6k75-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mp6k75-6.dist.dot'.
	Must remake target `mp6k75-6.dist.dot'.
	abyss-map -j10 -l64 mp6k_R1.mp.fastq.gz mp6k_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mp6k75-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mp6k75-6.dist.dot mp6k75-6.hist
	Successfully remade target file `mp6k75-6.dist.dot'.
	Considering target file `mp9k75-6.dist.dot'.
	File `mp9k75-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mp9k75-6.dist.dot'.
	Must remake target `mp9k75-6.dist.dot'.
	abyss-map -j10 -l64 mp9k_R1.mp.fastq.gz mp9k_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mp9k75-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mp9k75-6.dist.dot mp9k75-6.hist
	Successfully remade target file `mp9k75-6.dist.dot'.
	Considering target file `mpUnde75-6.dist.dot'.
	File `mpUnde75-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mpUnde75-6.dist.dot'.
	Must remake target `mpUnde75-6.dist.dot'.
	abyss-map -j10 -l64 mpUndetermined_R1.mp.fastq.gz mpUndetermined_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mpUnde75-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mpUnde75-6.dist.dot mpUnde75-6.hist
	Successfully remade target file `mpUnde75-6.dist.dot'.
	Considering target file `mp6k150-6.dist.dot'.
	File `mp6k150-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mp6k150-6.dist.dot'.
	Must remake target `mp6k150-6.dist.dot'.
	abyss-map -j10 -l64 mp6k150_R1.mp.fastq.gz mp6k150_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mp6k150-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mp6k150-6.dist.dot mp6k150-6.hist
	Successfully remade target file `mp6k150-6.dist.dot'.
	Considering target file `mp9k150-6.dist.dot'.
	File `mp9k150-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mp9k150-6.dist.dot'.
	Must remake target `mp9k150-6.dist.dot'.
	abyss-map -j10 -l64 mp9k150_R1.mp.fastq.gz mp9k150_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mp9k150-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mp9k150-6.dist.dot mp9k150-6.hist
	Successfully remade target file `mp9k150-6.dist.dot'.
	Considering target file `mpUnde150-6.dist.dot'.
	File `mpUnde150-6.dist.dot' does not exist.
	Pruning file `Ab10_10-6.fa'.
	Finished prerequisites of target file `mpUnde150-6.dist.dot'.
	Must remake target `mpUnde150-6.dist.dot'.
	abyss-map -j10 -l64 mpUndetermined150_R1.mp.fastq.gz mpUndetermined150_R2.mp.fastq.gz Ab10_10-6.fa \
	|abyss-fixmate -l64 -h mpUnde150-6.hist \
	|sort -snk3 -k4 \
	|DistanceEst --dot -j10 -k64 -l64 -s200 -n10 -o mpUnde150-6.dist.dot mpUnde150-6.hist
	Successfully remade target file `mpUnde150-6.dist.dot'.
	Finished prerequisites of target file `Ab10_10-6.path'.
	Must remake target `Ab10_10-6.path'.
	abyss-scaffold -k64 -s200 -n10 -g Ab10_10-6.path.dot Ab10_10-6.dot mp6k75-6.dist.dot mp9k75-6.dist.dot mpUnde75-6.dist.dot mp6k150-6.dist.dot mp9k150-6.dist.dot mpUnde150-6.dist.dot >Ab10_10-6.path
	Successfully remade target file `Ab10_10-6.path'.
	Finished prerequisites of target file `Ab10_10-7.adj'.
	Must remake target `Ab10_10-7.adj'.
	PathConsensus -k64 -p0.9 -s Ab10_10-7.fa -g Ab10_10-7.adj -o Ab10_10-7.path Ab10_10-6.fa Ab10_10-6.dot Ab10_10-6.path
	Successfully remade target file `Ab10_10-7.adj'.
	Considering target file `Ab10_10-7.path'.
	File `Ab10_10-7.path' was considered already.
	Considering target file `Ab10_10-scaffolds.fa'.
	File `Ab10_10-scaffolds.fa' does not exist.
	Pruning file `Ab10_10-7.adj'.
	Pruning file `Ab10_10-7.path'.
	Considering target file `Ab10_10-8.fa'.
	File `Ab10_10-8.fa' does not exist.
	Pruning file `Ab10_10-7.adj'.
	Pruning file `Ab10_10-7.path'.
	Pruning file `Ab10_10-6.fa'.
	Considering target file `Ab10_10-7.fa'.
	File `Ab10_10-7.fa' was considered already.
	Finished prerequisites of target file `Ab10_10-8.fa'.
	Must remake target `Ab10_10-8.fa'.
	cat Ab10_10-6.fa Ab10_10-7.fa \
	|MergeContigs -k64 -o Ab10_10-8.fa - Ab10_10-7.adj Ab10_10-7.path
	Successfully remade target file `Ab10_10-8.fa'.
	Finished prerequisites of target file `Ab10_10-scaffolds.fa'.
	Must remake target `Ab10_10-scaffolds.fa'.
	ln -sf Ab10_10-8.fa Ab10_10-scaffolds.fa
	Successfully remade target file `Ab10_10-scaffolds.fa'.
	Finished prerequisites of target file `scaffolds'.
	Must remake target `scaffolds'.
	Successfully remade target file `scaffolds'.
	Considering target file `scaffolds-dot'.
	File `scaffolds-dot' does not exist.
	Looking for an implicit rule for `Ab10_10-scaffolds.dot'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-8.dot'.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-8.dot'.
	Looking for a rule with intermediate file `Ab10_10-8.dot'.
	Avoiding implicit rule recursion.
	Trying pattern rule with stem `Ab10_10'.
	Trying implicit prerequisite `Ab10_10-7.adj'.
	Trying implicit prerequisite `Ab10_10-7.path'.
	Found an implicit rule for `Ab10_10-scaffolds.dot'.
	Pruning file `Ab10_10-7.adj'.
	Pruning file `Ab10_10-7.path'.
	Considering target file `Ab10_10-scaffolds.dot'.
	File `Ab10_10-scaffolds.dot' does not exist.
	Pruning file `Ab10_10-7.adj'.
	Pruning file `Ab10_10-7.path'.
	Considering target file `Ab10_10-8.dot'.
	File `Ab10_10-8.dot' does not exist.
	Pruning file `Ab10_10-7.adj'.
	Pruning file `Ab10_10-7.path'.
	Finished prerequisites of target file `Ab10_10-8.dot'.
	Must remake target `Ab10_10-8.dot'.
	PathOverlap --overlap --dot -k64 Ab10_10-7.adj Ab10_10-7.path >Ab10_10-8.dot
	Successfully remade target file `Ab10_10-8.dot'.
	Finished prerequisites of target file `Ab10_10-scaffolds.dot'.
	Must remake target `Ab10_10-scaffolds.dot'.
	ln -sf Ab10_10-8.dot Ab10_10-scaffolds.dot
	Successfully remade target file `Ab10_10-scaffolds.dot'.
	Finished prerequisites of target file `scaffolds-dot'.
	Must remake target `scaffolds-dot'.
	Successfully remade target file `scaffolds-dot'.
	Considering target file `stats'.
	File `stats' does not exist.
	Pruning file `Ab10_10-unitigs.fa'.
	Considering target file `Ab10_10-stats'.
	File `Ab10_10-stats' does not exist.
	Pruning file `Ab10_10-unitigs.fa'.
	Pruning file `Ab10_10-contigs.fa'.
	Pruning file `Ab10_10-scaffolds.fa'.
	Finished prerequisites of target file `Ab10_10-stats'.
	Must remake target `Ab10_10-stats'.
	abyss-fac Ab10_10-unitigs.fa Ab10_10-contigs.fa Ab10_10-scaffolds.fa |tee Ab10_10-stats
	Successfully remade target file `Ab10_10-stats'.
	Finished prerequisites of target file `stats'.
	Must remake target `stats'.
	Successfully remade target file `stats'.
	Pruning file `unitigs'.
	Pruning file `contigs'.
	Pruning file `contigs-dot'.
	Pruning file `scaffolds'.
	Pruning file `scaffolds-dot'.
	Pruning file `stats'.
	Finished prerequisites of target file `default'.
	Must remake target `default'.
	Successfully remade target file `default'.
	real 0m0.767s
	user 0m0.009s
	sys 0m0.025s

view raw biostars-165992.log hosted with ❤ by GitHub

[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.