Describe the bug
SAM file is not sorted ERROR even if the input file is sorted
cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t' '$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gzstdout:
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]
I'm sure that this error is from dnmtools instead of samtools
|
if (tid < prev_tid) throw dnmt_error("SAM file is not sorted"); |
I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
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Describe the bug
SAM file is not sorted ERROR even if the input file is sorted
stdout:
I'm sure that this error is from dnmtools instead of samtools
dnmtools/src/analysis/methcounts.cpp
Line 464 in e18ae72
I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?