This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Mapsplice 2 error

When running this command it shows error like this, I have all file in One folder. Please help me to resolve this problem

mapsplice.py -o outfuse --fusion --min-fusion-distance 200 -c bowtie2index.fa -x bowtie2index -1 SRR087416.fastq_filtered

[Mon Aug  6 12:07:02 2018] Beginning Mapsplice run (MapSplice v2.2.0)
[Mon Aug  6 12:07:02 2018] Bin directory: /home/prashant/anaconda2/bin/ 
[Mon Aug  6 12:07:02 2018] Preparing output location outfuse/
[Mon Aug  6 12:07:02 2018] Checking files or directory: SRR087416.fastq_filtered
[Mon Aug  6 12:07:02 2018] Checking files or directory: bowtie2index.fa/
Error: Could not find files or directory bowtie2index.fa/

Thank you

ngs rna-seq gene-fusion
• 2,086 views • link
updated by Ram Ram • written by amitunited0532 • amitunited0532

1 answer

Instead of -c bowtie2index.fa you need to provide the directory path where the 'bowtie2index.fa' is stored. If it is in current directory, you can just specify '-c ./'.

MapSplice user guide.

• 0 views • link
written by EagleEye EagleEye

I kept all files in one folder and also checked command which suggested. Again showed same error.

• 1 views • link
written by amitunited0532 • amitunited0532

Please report your recent command used and also the error log.

• 1 views • link
written by EagleEye EagleEye

Log in to answer this question.

More posts like this