Too few peaks in MACS2

[tamadp]

Hi everyone, I'm trying to call peaks with macs2 but run into the next warning when doing so:

"WARNING @ Tue, 14 Jun 2016 20:52:53: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.
WARNING @ Tue, 14 Jun 2016 20:52:53: Process for pairing-model is terminated! "

I am working with treatment and control samples, the number of reads for each is: 18448586 for control and 26581254 for treatment. All the reads are mapped and uniquely paired, as I already filtered them.

Could anyone explain the cause for the warning? I've tried to find information but haven't find many...Is the error related to the difference in number of reads? I thought macs scaled the samples automatically.

Thanks in advance!

Update: So I'm guessing this is the reason:
"DEBUG @ Thu, 16 Jun 2016 16:00:24: Number of unique tags on + strand: 627266
DEBUG @ Thu, 16 Jun 2016 16:00:24: Number of peaks in + strand: 19221
DEBUG @ Thu, 16 Jun 2016 16:00:24: Number of unique tags on - strand: 0
DEBUG @ Thu, 16 Jun 2016 16:00:24: Number of peaks in - strand: 0
DEBUG @ Thu, 16 Jun 2016 16:00:24: Chrom chr16 is discarded!"

And it happens for all the chromosomes. Any ideas on how to fix it?

[dpryan]

Can you post the first 10 or so alignments? Ideally you'll have a few with each orientation.

[tamadp]

Can you post the first 10 or so alignments? Ideally you'll have a few with each orientation.

Thanks for the reply, here it is:

D3YGT8Q1:296:C7M2RACXX:6:1105:5592:14554        99      chr1    9997    6       58M1I42M        =       10082   172     CCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
TAACCCTAACCCTAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC   BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIFFIBFFFIIBFBFFIBBBBFFBFBBFF<<<BFF<<BBFFB<<<BBF<BBBBB<BBFFFB07BB<<
B<BBB   AS:i:-12        XS:i:-11        XN:i:4  XM:i:4  XO:i:1  XG:i:1  NM:i:5  MD:Z:0N0N0N0N96 YS:i:-18        YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1205:20071:45553       99      chr1    9997    6       67M1I19M        =       10371   463     CCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
TAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAC BBBFFFFFFFBBFIBFFFFIIIBFFFFIIFIIIFFIIIIIFFFIIII<FFFFBFFIII<F0<BFB<7BFBF<BBBBFB<BBBFBB<B AS:i:-12        XS:i:-13
        XN:i:4  XM:i:4  XO:i:1  XG:i:1  NM:i:5  MD:Z:0N0N0N0N82 YS:i:-21        YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1211:19409:52344       99      chr1    9997    6       101M    =       10040   141     CCCCTACCCCTACCCCTACCCCTAACCCTAACCCTAACCCTAACCCTA
ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT   BBBFFFFFFFFFFFIIIIIIIIFFFFIIBFIIIIFFIIIIBFFIII<7FFFF707<BB7B'7BBBBBBBF'<<<BF<<BBFBBFB<7BBB<BBB<BBBFF7   
AS:i:-20        XS:i:-21        XN:i:4  XM:i:7  XO:i:0  XG:i:0  NM:i:7  MD:Z:0N0N0N0N2A5A5A82   YS:i:-5 YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1107:16167:27127       99      chr1    10002   1       70M     =       10038   106     AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
AACCCTAACCCTAACCCTAACC  BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIBFIIIIFFFFFFFFFF  AS:i:0  XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:70 
YS:i:0  YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1204:15589:43336       99      chr1    10002   1       94M     =       10020   112     AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT
AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC  BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIFIFIIIIIIIIIIIFFIIIIFFFFFFBFBFFFFFFFFFFFBFFFFFBFFFFBFFF  AS:i:0  XS:i:0  
XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:94 YS:i:0  YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1301:20602:31346       99      chr1    10003   0       5M1D43M1I6M1I24M1I8M    =       10065   129     ACCCTACCCTAACCCTAACCCTAACCCTAACC
CTAACCCTAACCCTAACCCCTAACCCCTACCCCTAACCCTAACCCTAACCCCTAACC       BBBFFFFFFFFFFFFFFIIFFFIIIIIFFBFFI07F<FI0B'BFF<F0BFF<7B'<B<B'707<BBBFBF<<<7BB7'77<<<B0700B       
AS:i:-35        XS:i:-30        XN:i:0  XM:i:1  XO:i:4  XG:i:4  NM:i:5  MD:Z:5^A54A26   YS:i:-4 YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1313:3132:51176        99      chr1    10003   1       34M1I60M        =       10351   384     ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACC
CTAACCCTAACCCTCACCCTAACCCTTACCCTAACCCTAACCCTAACCCTAACCC BBBFFBFFFFFFFFFFFFFFFIIFFIFFBBFFII7077FFFF07FFB077B<FF'0<B0'7<BFB<<'<0<<'0<BBBBBBBBBBB0<BBBBB7B AS:i:-14
        XS:i:-6 XN:i:0  XM:i:2  XO:i:1  XG:i:1  NM:i:3  MD:Z:53A11A28   YS:i:-2 YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:2103:13849:36280       99      chr1    10003   0       47M3I22M        =       10016   106     ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCACCCTACCCTGACCCTGACCCTGACC        BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIFIIIB7BFFIF77BB''7<<''7BBB'7BFFB'7BF<0'7<B        AS:i:-28        XS:i:-21        XN:i:0  XM:i:6  XO:i:1  XG:i:3  NM:i:9  MD:Z:42A3T0A5A5A5A3     YS:i:-24        YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:2212:8605:36420        99      chr1    10003   1       5M1D67M =       10152   225     ACCCTACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA        BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIFFIIIFFFFFFBFFF<BBFBFB        AS:i:-13        XS:i:-5 XN:i:0  XM:i:1  XO:i:1  XG:i:1  NM:i:2  MD:Z:5^A4T62    YS:i:0  YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:2313:18665:73233       99      chr1    10003   0       34M1I6M1I13M1I45M       =       10052   140     ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTTAACCCTTAACCCTGACCCTGACCCCTGACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC   BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIFF<FF7FB<BFBFBB'7BFFBBFFFFBFFF<F<0<BBBB7<BBBB<<BBB7B<BFBB70BBBFBBB   AS:i:-39        XS:i:-28        XN:i:0  XM:i:3  XO:i:3  XG:i:3  NM:i:6  MD:Z:47A6A4A38  YS:i:-5 YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1107:9298:15688        99      chr1    10004   1       39M     =       10398   433     CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC BBBFFFFFFFFFFIIIFIFFIIIFFIIFFFFFFIBFFFI AS:i:0  XS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:39 YS:i:0  YT:Z:CP
D3YGT8Q1:296:C7M2RACXX:6:1210:18787:54611       99      chr1    10004   2       22M1D79M        =       10261   359     CCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTACCCCTGACCCTGACCCTGACCCTGACCCTGACCCTGACCCTAACCCTAACCCTAA   BBBFFFFFFFFFFIIIIIIIIFIIIIIIIIIIIFFIIIFFFFFIFFIFFFIBBFFIFBFFFFFBFFFFFBBFFFBBBBFBFB0BBBB77BBBF77BBBBBB   AS:i:-44        XS:i:-42        XN:i:0  XM:i:7  XO:i:1  XG:i:1  NM:i:8  MD:Z:22^A24A4A5A5A5A5A5A19      YS:i:-18        YT:Z:CP

[tamadp]

So, I didn't realise the format needed to be specified for paired ends and I managed to make it work by running the "-f BAMPE" command. However, macs is still not building the R model, any reason why?