problem with bismark on sorted.bam

[ppswang]

Hi,

I am testing the msPIPE docker app on a small test of test data.

I ran into problem here:

3. Calling (bismark) .. start
$ /msPIPE/bin/Bismark/bismark_methylation_extractor -p --no_overlap --comprehensive --gzip --CX --cytosine_report --genome_folder /msPIPE/reference/hg38/ -o /results/methylCALL/blood-1/methylcontext /results/methylCALL/blood-1/data/blood-1_bismark.sorted.bam

Now testing Bismark result file >/results/methylCALL/sperm-2/data/sperm-2_bismark.sorted.bam< for positional sorting (which would be bad...)    

*** There's a problem executing the upper command.
*** check logfile > /results/methylCALL/blood-1/logs/log.Bismark_call.txt

And the Bismark log file shows:

Checking file >>/homes/paul.wang/results/methylCALL/blood-2/data/blood-2_bismark.sorted.bam<< for signs of file truncation...

The IDs of Read 1 (HWI-ST552:285:CA6UAACXX:5:1205:2572:17001) and Read 2 (HWI-ST552:282:CA4GPACXX:8:1315:8756:81934) are not the same. This might be the result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extrac
tion. Please use an unsorted file instead or sort the file using 'samtools sort -n' (by read name). This may also occur using samtools merge as it does not guarantee the read order. To properly merge files please use 'samtools merge -n' or 'samtools cat'.

[RouleThomas]

Same issue here, any update?