Question: Bowtie2: Error: No input read files were valid
1
gravatar for 200dumplings
18 months ago by
200dumplings10
200dumplings10 wrote:
bowtie2 -x mm10 -q -1 /PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_1.fastq -2 /PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_2.fastq -S H3K4ME1_NATIVE_A03.sam
ERROR:
stat: Bad file descriptor
Warning: Could not open read file "/PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_1.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
  

Question: The fastq samples files seem to be fine, as they could be read by fastqc. I was wondering what went wrong here?

chip-seq bowtie2 • 955 views
ADD COMMENTlink modified 18 months ago by h.mon31k • written 18 months ago by 200dumplings10

Do you actually have a folder structure that looks like this /PX0315/C89CJANXX_2/PX0315_AACCCC/?

If you do head -4 /PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_1.fastq what does it show?

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax91k

Sounds like a wrong path. /PX0315 would be a non-standard root directory which is unlikely.

ADD REPLYlink written 18 months ago by ATpoint40k

Did you make sure that you've given that directory permissions to write to the files in that directory? You should also simplify your directories, because that could be a headache to deal with :)

ADD REPLYlink written 18 months ago by Poetic_Premium60

Yes hahah I fixed it by giving it the actual directory. Thank you!

ADD REPLYlink written 17 months ago by 200dumplings10
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