Cannot open file.fasta. Now exit to system...

Question

[sansan_96]

Hi, I'm trying to run SOAPdenovo but I get the following:

user@DESKTOP-05K13O7:~/agave/crudos/ensamble$ SOAPdenovo-Trans-1.0.5/SOAPdenovo-Trans-31mer all -s config_file -o output_prefix

Version 1.04

pregraph -s config_file -o output_prefix
In config_file, 1 libs, max seq len 100, max name len 256

8 thread created in prlHashReads
read from file - type 2:
P248H_R1_001.fasta
read from file - type 2:
P248H_R2_001.fasta
Cannot open P248H_R1_001.fasta. Now exit to system...

My config_file is:

#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which order the reads are used
asm_flags=3
#fastq file for read 1
q1= P248H_R1_001.fasta
#fastq file for read 2
q2= P248H_R2_001.fasta

My directory:

user@DESKTOP-05K13O7:~/agave/crudos/ensamble$ ls -l

total 35800736
-rw-r--r-- 1 user user 6835412619 Nov 2 23:33 P248H_R1_001.fasta
-rw-r--r-- 1 user user 11494548882 Nov 2 23:13 P248H_R1_001.fastq
-rw-r--r-- 1 user user 6835412619 Nov 2 23:35 P248H_R2_001.fasta
-rw-r--r-- 1 user user 11494548882 Nov 2 23:14 P248H_R2_001.fastq
drwxr-xr-x 4 user user 4096 Nov 2 23:26 SOAPdenovo-Trans-1.0.5
-rw-r--r-- 1 user user 317 Nov 2 23:35 config_file

Can you help me?

Answer 1

[JC]

In your config file, you have a space before the file name, maybe that is the problem. Also could be better to use the full path to the file.