ReadAlignChunk_processChunks.cpp:115:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >

[ranijames]

Dear All,
I am using STAR aligner to align a single fastq file, using default parameters on 2-pass mode. But it is throwing following error,
ReadAlignChunk_processChunks.cpp:115:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >
Any help or advice would be great
Thank you

[alexdobin]

Hi @ranijames,

it seems you have a problem with the fastq files formatting. Please try to unzip your files before mapping and look at first few lines. If they look OK, try to map one read with --readMapNumber 1.
If it does not work, please send me the Log.out file.

Cheers
Alex

[santiagosnchez]

It would be nice to have ZLIB compression/decompression support. Having to decompress all your fastq file can be burdensome on small systems.

[alexdobin]

Hi Santiago,

at the moment, you can use --readFilesCommand zcat to unzompress the gzipped files on-the-fly.

Cheers
Alex

[jshaik1979]

The issue is not with the files themselves. The issue is with compression. STAR doesn't support compressed files. I had the same issue. works fine after unzipping the fastq files

[alexdobin]

With compressed files, STAR uses system command (such as zcat) to decompress files, and fifo files to input the uncompressed stream. It may not work on systems that do not support fifo files (such as Windows partitions).

[lcolladotor]

Uncompressing with zcat prior to running STAR helped us work around this issue on a SGE cluster. Might be the fifo issue you mentioned last year. Anyway, thank you for this thread!