Hello,
I'm getting an error: "sambamba-view: not enough data in stream" by running sambamba-sort, below my script :
PS: I get this error only for some bam files but for all !!
"sambamba view -t ${NCPU} -f bam -F \"not (unmapped or mate_is_unmapped) and mapping_quality >=0\" ${BAMIN} ${chroms} | \
glia -Rru -w 1000 -S 100 -Q 100 -G 4 -f ${REFFASTA} -v ${KNOWN_INDELS} | \
sambamba sort -t ${NCPU} -m 2GB --tmpdir=${SOUTDocker}/tmp -o ${SOUTDocker}/alignments/${BAM_PREFIX}.dupemk.${REALN}.bam /dev/stdin && \
sambamba index ${SOUTDocker}/alignments/${BAM_PREFIX}.dupemk.${REALN}.bam && \
sambamba flagstat -t ${NCPU} ${SOUTDocker}/alignments/${BAM_PREFIX}.dupemk.${REALN}.bam > ${SOUTDocker}/reports/${BAM_PREFIX}.dupemk.${REALN}.bam.flagstat && \
bedtools bamtobed -i ${SOUTDocker}/alignments/${BAM_PREFIX}.dupemk.${REALN}.bam | bedtools merge > ${SOUTDocker}/reports/${BAM_PREFIX}.dupemk.${REALN}.bed && \
rm -rf ${SOUTDocker}/tmp/*"
Is my syntax wrong?
Thank you.
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