Hi, I ran BAMSurgeon (https://github.com/adamewing/bamsurgeon), and it gives the following error report:
ERROR 2017-07-06 09:03:39.934250 encountered error in mutation spikein: ['chr1_27691816_27691816_0.5_None']
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/bamsurgeon-1.0-py2.7.egg/EGG-INFO/scripts/addsnv.py", line 275, in makemut
File "build/bdist.linux-x86_64/egg/bamsurgeon/aligners.py", line 67, in remap_bam
remap_bwamem_bam(bamfn, threads, fastaref, picardjar, mutid=mutid, paired=paired)
File "build/bdist.linux-x86_64/egg/bamsurgeon/aligners.py", line 210, in remap_bwamem_bam
raise ValueError("ERROR\t" + now() + "\t" + mutid + "\tbam readcount < fastq readcount, alignment sanity check failed!\n")
ValueError: ERROR 2017-07-06 09:03:39.933970 haplo_chr1_27691816_27691816 bam readcount < fastq readcount, alignment sanity check failed!
This error report does not appear all the time, but about one out of several spikeins. I looked through the BAMSurgeon github, and did not find the answer.
If you know how to fix it, could you please share with me your solution? Thanks for your help in advance!