I would reverse the order of the last two arguments to samtools sort,
and use the -o flag to specify the output file name. Thus,
samtools view -bS SMDC-1_aln-pe.sam | samtools sort -m 30000000000 -o
SMDC-1_sorted -
Can't help with samtools view not finding "SMDC-1_aln-pe.sam".
That's probably a typing error or a directory path issue. Could be
a permissions problem, but that's most unlikely.
- tom blackwell -
On Thu, 11 Jun 2015, ???? Fang Liu wrote:
Dear all,
I just started analyzing my RNA-seq results,
first, I used command
bwa mem -t 20 transmycale95300.fasta SMDC-1_R1_shortReadRemoved.fq
SMDC-1_R2_shortReadRemoved.fq > SMDC-1_aln-pe.sam
to generate sam files for downstream analysis. But then when I ran samtools, it
says there???s something wrong with my sam file.
samtools view -bS SMDC-1_aln-pe.sam | samtools sort -m 30000000000 -
SMDC-1_sorted
[bam_header_read] EOF marker is absent. The input is probably truncated.
[main_samview] fail to open "SMDC-1_aln-pe.sam" for reading.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)
Can anyone tell me how to solve this? Many thanks!
Kind. Fang
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