SSPACE bowtie and bwa error

Question

[milady81]

I want to run the SSPACE prescaffolding, my library is:

(microorganism genome)

lib1 bowtie R1.fastq R2.fastq 250 0.5 FR

and the command line:

perl ../app/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl \
     -l library_sspace.txt \
     -s ../MaSuRCA/Illumina_masurca_celera_scf.fasta \
     -b masu_celera \
     -T 8 -x 0 -k 5 -z 100 \
     -a 0.7 -m 35 -o 20 -v 1

I am getting an error:

=>Fri Jun 21 14:33:11 2019: Building Bowtie index for contigs

Bowtie-build error; -1 at /bioinf/proj_data_chestnut/dorota_b/app/SSPACE-STANDARD-3.0_linux-x86_64/bin/PairingAndScaffolding.pl line 80.
**************************************************
Process 'mapping reads' failed on Fri Jun 21 14:33:12 2019

At the internet I found that maybe it is a problem with the chmod, I did chmod to the SSPACE folder it is now:

drwxr-xr-x  2 dorota user 4096 Jun 11 12:34 SSPACE-LongRead_v1-1
drwxrwxrwx  8 dorota user 4096 Jun 17 17:53 SSPACE-STANDARD-3.0_linux-x86_64

Still, the same error.
I know there is a similar question to mine however no help and no answer.
I would be very glad if someone helps me, I am trying to solve the issue for two days and now I am getting pissed off.

btw. the same problem/error with the -x 0 and -x 1 (extension of the contig)

Please help me,
Dorota

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[milady81]

Thank you, will do it in the future:) Sorry for taking your time

Answer 1

[hnt001]

Hello,

I know this might be too late for you but I just wanted to put it here so who still has this problem would take advantage.

To solve this problem, you would have to install Bowtie if you already have bowtie2 installed. I believe the program is still running on the old version of bowtie. I was able to run after installing bowtie via conda.

I hope it helps!