Bowtie2: Error: No input read files were valid
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?
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h.mon
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200dumplings •
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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.fastqwhat does it show?Sounds like a wrong path.
/PX0315would be a non-standard root directory which is unlikely.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 :)
Yes hahah I fixed it by giving it the actual directory. Thank you!