bam- readcount error

Question

[mark.rose]

When running bam-readcount I get (minus the 8M previous warnings of the same type):

WARNING: In read m151222_205817_42179_c100908792550000001823210904291644_s1_p0/4606/0_7297: Couldn't find the generated tag.
WARNING: In read m151222_205817_42179_c100908792550000001823210904291644_s1_p0/3398/0_2955: Couldn't find the generated tag.
GA21-EcoRV      17329   t       149     =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  T:149:254.00:12.11:254.00:77:72:0.00:0.05:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00

So, I've read on line that such warnings can be ignored, however, only results on one position are produced

Thanks

[mark.rose]

I am adding one line from the corresponding sam file as it may help. I am removing the sequence and qualities for readability (these are long pacbio reads.

m151222_205817_42179_c100908792550000001823210904291644_s1_p0/25/477_7645       0       GA21-EcoRV      1       254     4598S12M1D1M1D9M1I19M1D15M1D9M1I4M1D20M1D10M1I6M1D18M2I3M1I3M1D7M1I16M1I6M1D55M1I7M1I42M1D45M1I17M2I3M1I12M1I2M1D7M1D5M1I2M1I44M1I9M1D15M1D19M1D4M1I4M1I33M1I15M1D14M1D6M1D5M1I19M1D11M1I8M1D8M1I4M1I7M1I87M1I40M1I19M1D2M2I3M1I6M1I17M1I43M1D12M1I29M1D23M1D3M1D7M1I30M1I4M1I3M2I26M1I34M1D15M1I37M1I14M1I12M2I1M1I6M1I16M1D13M1D6M1D43M2I18M1D8M1D2M1D10M1D33M1I8M1D7M1D5M2D13M2I28M1I4M1D4M1D10M1I1M1I59M1I5M1I4M1I30M1D55M3I36M1I12M1D11M1D3M1D2M1I5M1D12M1D27M1D10M1I11M1I18M1D5M1D25M1I9M1I18M1I8M1D1M1I7M1I4M1I1M1D5M1I9M1I3M1D11M1D82M1I12M1D3M1D20M2I11M1I104M1D19M1D7M1D15M1I38M1I12M1D9M1D53M1I21M1I20M1I25M1D5M1I24M1I15M1I11M1I2M1D9M1I3M1I1M1I75M1I21M1D5M1D6M1D16M1D5M1I40M1D10M1I3M1I27M1D6M1I19M2I6M1I6M19S        *       0       2521   <sequence removed>  <qualities removed>  RG:Z:de3b3891cb AS:i:-11285     XS:i:1  XE:i:7169       XL:i:2551       XT:i:1NM:i:179        FI:i:4599       XQ:i:7168

Answer 1

[ernfrid]

This error indicates that bam-readcount's internal mechanisms for caching per-read statistics are failing and that is likely the reason your results are incorrect. This is due to a bug in calling bam-readcount without requesting a region. For your case, a decent workaround may be to just request the entire "chromosome" like so: bam-readcount -f ref.fa your.bam GA21-EcoRV