Bowtie2: Error: No input read files were valid

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5.0 years ago

200dumplings ▴ 10

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 • 4.5k views

ADD COMMENT • link updated 5.0 years ago by h.mon 35k • written 5.0 years ago by 200dumplings ▴ 10

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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.fastq what does it show?

ADD REPLY • link 5.0 years ago by GenoMax 141k

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

ADD REPLY • link 5.0 years ago by ATpoint 82k

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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 :)