Problem with utf-8 Unicode

simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

https://htseq.readthedocs.io/en/release_0.11.1/

GNU General Public License v3.0

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Problem with utf-8 Unicode #49

Closed crikkia closed 6 years ago

crikkia commented 6 years ago

Hi,

I try to run htseq-count from my MacOs. I am using python3.6. When I type the command line htseq-count --stranded=no file.bam file.gft hstseq starts the run and after processing the gtf file, it gave me this error: Error occurred when reading beginning of SAM/BAM file 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte [Exception type: UnicodeDecodeError, reaised in codecs.py:321]

The bam file is sorted by name

Any idea how to solve this?

crikkia commented 6 years ago

I found the solution. I did not add the --format option to tell that my file was .bam.

Sorry!