Error in Cuffdiff

Question

[harshraje19]

Dear friends,

I got following warning/error after running the cuffdiff. can anyone help to solve this error. Command is written above the warning/erro

Thanks

harshraj@harshraj-XPS-8930:~/ArabidopsisExpt$ cuffdiff -o Cuffdiff_out -u cuffmerge_out/merged.gtf control1_thout/accepted_hits.bam, control2_thout accepted_hits.bam, treated1_thout, accepted_hits.bam, treated2_thout/accepted_hits.bam
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
terminate called after throwing an instance of 'std::__ios_failure'
  what():  basic_filebuf::underflow error reading the file: iostream error
Aborted (core dumped)

[GenoMax]

Looks like there is an error in your command line. These file paths don't seem to be correct

control1_thout/accepted_hits.bam, control2_thout accepted_hits.bam, treated1_thout, accepted_hits.bam, treated2_thout/accepted_hits.bam

most likely you need

control1_thout/accepted_hits.bam,control2_thout/accepted_hits.bam treated1_thout/accepted_hits.bam,treated2_thout/accepted_hits.bam

Files separated by comma need to be replicates. If they are all independent then no commas should be used.

[harshraje19]

I still have similar error as

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). terminate called after throwing an instance of 'std::__ios_failure' what(): basic_filebuf::underflow error reading the file: iostream error Aborted (core dumped)

[GenoMax]

So are those files actually in the paths you are indicating they are at in the command line above?

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