bowtie2 alignments "Error: No input read files were valid"

Question

[luzglongoria]

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?

Answer 1

[Devon Ryan]

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

Answer 2

[GenoMax]

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.