Question: bowtie2 alignments "Error: No input read files were valid"
0
gravatar for luzglongoria
2.2 years ago by
luzglongoria40
luzglongoria40 wrote:

Hi there,

I am doing an alignment with bowtie2 and with several end-paired reads. I write this command:

bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace/reference_genomes/parasitereference.fasta -q -k 1 --al aligned_reads.fastq -1 /home/luz_garcia_longoria/workspace/s21_1.fq,s22_1.fq,s23_1.fq,s24_1.fq,s25_1.fq,s31_1.fq,s32_1.fq,s33_1.fq,s34_1.fq,s35_1.fq -2 /home/luz_garcia_longoria/workspace/s21_2.fq,s22_2.fq,s23_2.fq,s24_2.fq,s25_2.fq,s31_2.fq,s32_2.fq,s33_2.fq,s34_2.fq,s35_2.fq > aligned_host_parasite.sam | samtools view -b -o aligned_host_parasite.bam

and then I get this error message:

stat: No such file or directory
Warning: Could not open read file "s22_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s23_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s24_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s25_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s31_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s32_1.fq" for reading; skipping...
stat: No such file or directory
Warning: Could not open read file "s33_1.fq" for reading; skipping...
 stat: No such file or directory
 Warning: Could not open read file "s34_1.fq" for reading; skipping...
 stat: No such file or directory
 Warning: Could not open read file "s35_1.fq" for reading; skipping...
stat: No such file or directory
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1

What is wrong in my command?

error rna-seq bowtie2 • 1.9k views
ADD COMMENTlink modified 2.2 years ago by Devon Ryan97k • written 2.2 years ago by luzglongoria40
2
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

You need the full path for each of the files separated by commas.

ADD COMMENTlink written 2.2 years ago by Devon Ryan97k
1
gravatar for genomax
2.2 years ago by
genomax92k
United States
genomax92k wrote:

Unless you are in /home/luz_garcia_longoria/workspace directory when you issue the bowtie2 command you are going to have to affix that path before every file name in you command.

/home/luz_garcia_longoria/workspace/file1.fq,/home/luz_garcia_longoria/workspace/file2.fq,/home/luz_garcia_longoria/workspace/file3.fq etc.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax92k
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