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I used BWA for alignment and then used the sam generated by BWA for alignment, but I am getting the following error
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at IWGSC_CSS_1DL_scaff_2280152:6081, last one was at IWGSC_CSS_1DL_scaff_2280152:6084
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at IWGSC_CSS_1DL_scaff_2280152:6081, last one was at IWGSC_CSS_1DL_scaff_2280152:6084
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.