No common chromosome names can be found from treatment and control! Check your input files! MACS will quit...

[EPKok]

Hi. I received the following error when performing macs2 callpeaks

INFO  @ Wed, 24 Oct 2018 17:15:52: #1.2 read input tags...
INFO  @ Wed, 24 Oct 2018 17:15:52: #1 tag size is determined as 150 bps
CRITICAL @ Wed, 24 Oct 2018 17:15:52: No common chromosome names can be found from treatment and control! Check your input files! MACS will quit...
CRITICAL @ Wed, 24 Oct 2018 17:15:52: Chromosome names in treatment: chr10,chr18,chr2,chr3
CRITICAL @ Wed, 24 Oct 2018 17:15:52: Chromosome names in control:

I used the same reference genome for BWA mapping of both treatment and control. I extracted the header of the BAM as below: Treatment:

@HD     VN:1.5  SO:coordinate
@SQ     SN:chr1 LN:249250621
@SQ     SN:chr2 LN:243199373
@SQ     SN:chr3 LN:198022430
@SQ     SN:chr4 LN:191154276
@SQ     SN:chr5 LN:180915260
@SQ     SN:chr6 LN:171115067
@SQ     SN:chr7 LN:159138663
@SQ     SN:chr8 LN:146364022
@SQ     SN:chr9 LN:141213431
@SQ     SN:chr10        LN:135534747
@SQ     SN:chr11        LN:135006516
@SQ     SN:chr12        LN:133851895
@SQ     SN:chr13        LN:115169878
@SQ     SN:chr14        LN:107349540
@SQ     SN:chr15        LN:102531392
@SQ     SN:chr16        LN:90354753
@SQ     SN:chr17        LN:81195210
@SQ     SN:chr18        LN:78077248
@SQ     SN:chr19        LN:59128983
@SQ     SN:chr20        LN:63025520
@SQ     SN:chr21        LN:48129895
@SQ     SN:chr22        LN:51304566
@SQ     SN:chrM LN:16571
@SQ     SN:chrX LN:155270560
@SQ     SN:chrY LN:59373566

Control:

@HD     VN:1.5  SO:coordinate
@SQ     SN:chr1 LN:249250621
@SQ     SN:chr2 LN:243199373
@SQ     SN:chr3 LN:198022430
@SQ     SN:chr4 LN:191154276
@SQ     SN:chr5 LN:180915260
@SQ     SN:chr6 LN:171115067
@SQ     SN:chr7 LN:159138663
@SQ     SN:chr8 LN:146364022
@SQ     SN:chr9 LN:141213431
@SQ     SN:chr10        LN:135534747
@SQ     SN:chr11        LN:135006516
@SQ     SN:chr12        LN:133851895
@SQ     SN:chr13        LN:115169878
@SQ     SN:chr14        LN:107349540
@SQ     SN:chr15        LN:102531392
@SQ     SN:chr16        LN:90354753
@SQ     SN:chr17        LN:81195210
@SQ     SN:chr18        LN:78077248
@SQ     SN:chr19        LN:59128983
@SQ     SN:chr20        LN:63025520
@SQ     SN:chr21        LN:48129895
@SQ     SN:chr22        LN:51304566
@SQ     SN:chrM LN:16571
@SQ     SN:chrX LN:155270560
@SQ     SN:chrY LN:59373566

I don't really see the difference between the header of the treatment and control.

[taoliu]

It seems MACS2 can't read any usable reads from the control BAM file. Could you post the 'samtools flagstat' of your BAM files?

[EPKok]

Please find below the stats:

53939146 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
45172510 + 0 mapped (83.75% : N/A)
53939146 + 0 paired in sequencing
26969573 + 0 read1
26969573 + 0 read2
0 + 0 properly paired (0.00% : N/A)
45172510 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
485738 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I have found that no tag is actually detected from the BAM file. Could the BAM file be corrupted?

[taoliu]

It seems that none of the reads can be properly paired, although they can be mapped to the genome. Definitely strange.

[EPKok]

Finally, I managed to get properly paired reads by including -a 1200 for bwa sampe.

[bilalahmad252]

Getting the same error. Can you please help how to fix. Thanks!