Gundala Viswanath wrote on 02/22/2017 06:01 AM: > samtools view -h ~/bar-something-data/myfile.bam > > ~/bar-something-data/test.sam > > It gave the following error: > samtools: writing to standard output failed: Invalid argument > samtools: error closing standard output: -1
It is good practice not to use ~ in complex commands because it is interpreted differently depending on the shell. Have you tried using full path, for example: samtools view -h /home/ubuntu/bar-something-data/myfile.bam > /home/ubuntu/bar-something-data/test.sam Are you able to otherwise write in that directory? Try: touch /home/ubuntu/bar-something-data/foo which should create an empty file without any error messages. Please also provide the output of "mount" command. ------------------------------------------------------------------------------ Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
