So I have 4 32 mer Illumina seq files each around 9.5gb each in fastQ format. TopHat runs exceedingly slow for 2 of them and outputs files that are useable by cufflinks and samtools. The other two run quite quickly and possess all of the same files(no errors in the logs) and the juncs and coverage files are all in good order. The only difference I can find is that the size of accepted_hits.sam is ~3gb for the failed files and ~1 for the successful files.
If i run cufflinks on these files I get the following error:
cufflinks /home/james/Desktop/TophatAlignments2010/SRX002556-g1/accepted_hits.sam
Counting hits in map
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at Chr1:7405, last one was at Chr1:66939
If I run sam tools I get this error:
samtools sort /home/james/Desktop/TophatAlignments2010/SRX002556-g1/accepted_hits.sam /home/james/Desktop/accepted_hits.sam
[bam_header_read] EOF marker is absent.
[bam_sort_core] truncated file. Continue anyway.
Segmentation fault
Has anyone come across this problem?
If i run cufflinks on these files I get the following error:
cufflinks /home/james/Desktop/TophatAlignments2010/SRX002556-g1/accepted_hits.sam
Counting hits in map
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at Chr1:7405, last one was at Chr1:66939
If I run sam tools I get this error:
samtools sort /home/james/Desktop/TophatAlignments2010/SRX002556-g1/accepted_hits.sam /home/james/Desktop/accepted_hits.sam
[bam_header_read] EOF marker is absent.
[bam_sort_core] truncated file. Continue anyway.
Segmentation fault
Has anyone come across this problem?
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