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From: Sendu B. <sb...@sa...> - 2011-11-17 15:16:48
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Actually, in this case the warning should be ignored. Using samtools view -u gives uncompressed bam, and these do not have the EOF marker. On 17 Nov 2011, at 14:43, Ivan Gregoretti wrote: > Hello 王森, > > That means that the bam file has a problem. It is truncated, meaning incomplete. > > Very big files do get corrupted occasionally. You need to create the > bam file again. > > I hope this helps. > > Ivan > > 2011/11/16 王森 <wa...@bi...>: >> >> >> hi, >> What does this error mean with respect to the completion of my samtools >> command(samtools sort )? >> why? >> [bam_header_read] EOF marker is absent. The input is probably truncated. >> The commmand: >> samtools view -buS -T all.fa -o s_5_1.bam s_5_1.sam > log >> samtools sort -n s_5_1.bam s_5_1.sort > sort.log >> Thank you! |