MACS2 run error: ZeroDivisionError: integer division or modulo by zero & TypeError: an integer is required
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Joseph Sarro
Jun 20, 2014, 12:08:37 PM6/20/14
to macs-ann...@googlegroups.com
I am getting an error when I try running the callpeak function in MACS2. I tried using the BWA generated SAM files and I also tried making them BAM
files. I also tried removing unmapped reads from the SAM files using
samtools view -F 4. I also tried re-installing the software, pip outputs all requirements satisfied. I have multiple sam files ranging from 120-155G.
Below are my errors and the tail output of my sam file. Has anyone come across this in MACS2 before?
Thanks,
Joe-
Below are my errors and the tail output of my sam file. Has anyone come across this in MACS2 before?
Thanks,
Joe-
When I try running it with BAM files I get the following output
Traceback (most recent call last):
File "/afs/crc.nd.edu/user/local/bin/macs2", line 557, in <module>
main()
File "/afs/crc.nd.edu/user/local/bin/macs2", line 56, in main
run( args )
File "/afs/crc.nd.edu/user/local/lib/python2.7/site-packages/MACS2/callpeak.py", line 70, in run
else: (treat, control) = load_tag_files_options (options)
File "/afs/crc.nd.edu/user/local/lib/python2.7/site-packages/MACS2/callpeak.py", line 379, in load_tag_files_options
tp = options.parser(options.tfile[0], buffer_size=options.buffer_size)
File "cParser.pyx", line 667, in MACS2.IO.cParser.BAMParser.__init__ (MACS2/IO/cParser.c:8235)
File "/afs/crc.nd.edu/x86_64_linux/python/2.7.4/lib/python2.7/gzip.py", line 258, in read
if not self._read(readsize):
File "/afs/crc.nd.edu/x86_64_linux/python/2.7.4/lib/python2.7/gzip.py", line 293, in _read
self._read_gzip_header()
File "/afs/crc.nd.edu/x86_64_linux/python/2.7.4/lib/python2.7/gzip.py", line 205, in _read_gzip_header
self._read_exact(struct.unpack("<H", self._read_exact(2)))
File "/afs/crc.nd.edu/x86_64_linux/python/2.7.4/lib/python2.7/gzip.py", line 185, in _read_exact
data = self.fileobj.read(n)
TypeError: an integer is required
and with a SAM file
Traceback (most recent call last):
File "/afs/crc.nd.edu/user/local/bin/macs2", line 557, in <module>
main()
File "/afs/crc.nd.edu/user/ocal/bin/macs2", line 56, in main
run( args )
File "/afs/crc.nd.edu/user/local/lib/python2.7/site-packages/MACS2/callpeak.py", line 70, in run
else: (treat, control) = load_tag_files_options (options)
File "/afs/crc.nd.edu/user/local/lib/python2.7/site-packages/MACS2/callpeak.py", line 381, in load_tag_files_options
ttsize = tp.tsize()
File "cParser.pyx", line 189, in MACS2.IO.cParser.GenericParser.tsize (MACS2/IO/cParser.c:3371)
ZeroDivisionError: integer division or modulo by zero
the tail of my sam file looks like
CD1V1KACXX:7:2316:21368:100847#NNNNNNN 77 * 0 0 * * 0 0 GATGACGATTTGGACGGAAAACANTATGCTTGCGAGTTAATTNATGTCGAATTGAAATCTATTTCTGGTAGCGAGTCTCTTTTTNNNATTACTGTTGATT [__VcZcZe^aaaX`ddeedeedBPY^P^aae[Yc_OGHHNWBLLT_dZ\dV^`YZZVZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
FCD1V1KACXX:7:2316:21368:100847#NNNNNNN 141 * 0 0 * * 0 0 NTTAACATTTTTAAAGTACTTTAGATNNNNNNCTTAACTCACCANNNNNNNNNCTAAAAANAAACTCTCNACCAGCCCTATATTTNCATTCTNNNNNNNN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 113 supercont1.3762 35 20 100M = 40 5 ACCATGCTGAGATGATCATTCACTTACTTTCAGAGCAACACTGCTTTTTTGCTGTAGAACATAGTAGCCTGGATTACTTTGATCTATTCTATCCACCAGG aaa`_]`Yaa`bc_R_adcaZVZ^\^b]`RddbS_\b\_\_be[de_df_hf]bhhhfea_edbffdee[gdb[c`[d^Y[Sb_dddYb[cWc`Jcc___ XT:A:U NM:i:79 SM:i:20 AM:i:20 X0:i:1 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C1A0T0G1T0G0C0G0C1G0C0T0C0G0G0G0C0T0G0G0C0C0G0A1G0A0G0G0A0T1A0T0C0T0G1A2A0G0C2G0C0G0C0T0C0G0C0T0G0G0T1T0C0C2G0T3T0G0A0G1A0G0G0C0G0C0A0G0T1G2C0C0A0G0C0A1G0T0C0 XA:Z:supercont1.3762,-4,100M,1;supercont1.3762,-16,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 177 supercont1.3762 40 37 100M = 35 -5 GATCAAAGTAATCCAGGCTACTATGTTCTACAGCAAAAAAGCAGTGTTGCTCTGAAAGTAAGTGAATGATCATCTCAGCATGGTTTAGACTTTGTTATTA bbbbc`bbbbb`b`db_c`Yeegggdcegdhhhhhgf`bWddhhheaXOIecfggghhhhhfdf`bfbXfffhffhhhdhghgdffeb[Z^cccaee___ XT:A:U NM:i:79 SM:i:37 AM:i:20 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1T0G1G0C2C0T0C0G0G0G0C0T1G0C0C0G0A0T0G0A0G0G0A1G0A0T0C0T0G0C1G0C3T0T0G0C0G0C0T1G3G0T0T0T0C0C2G0T0T0G0G0T0G0A0G0C0A0G0G1G0C0A0G1T1C1C0C0A0G1A0C0G0T0C0G0G0G0C0G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 113 supercont1.3762 2 7 100M = 8 6 AAACGTTACAATTAATTTTCGACAAAATTGCAATTTTGGGCTTGAACCAAATTAATCATGTAAAAAATTGGCAAAATTGTTACCTTGACTTTCTATTGAC BBBa`b_]``bbbb`XTZZ]adgdb`dbfcgcbe`ge_ZaWbegfaShhhgfhhhehhhefghhhhhfgdfhhhhhhhhhgedfddecgggeaccee__b XT:A:U NM:i:77 SM:i:7 AM:i:7 X0:i:1 X1:i:39 XM:i:0 XO:i:0 XG:i:0 MD:Z:0G0C0T0G0C0G0C0C0A0G0T0G0G0C0T0C0C0A0G2C0G0G0G0G0C1G2G1C0C0A3T0G0C0G0C1G1T0C0G0G0G0C0T0G0G1C0G0A1G1G0G1T0G0A0T0C0T0G0C1G0C0A1C1T0G1G0C0T0C0G0C1G0G1T1C0C1G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 177 supercont1.3762 8 7 100M = 2 -6 CCAATTTTTTACATGATTAATTTGGTTCAAGCCCAAAATTGCAATTTTGTCGAAAATTAATTGTAACGTTTCATTTTCCCCGACCACTGGAAGCATGATG _]_aabbdcb`Y]bbcbbbbaaaabbaa`_`]ac_^Z]_d`degghhgeZfhffhgec[cbbaaZaf_hhhhhhgffgagfhbhhhfgcegecaccc___ XT:A:U NM:i:76 SM:i:7 AM:i:7 X0:i:1 X1:i:38 XM:i:0 XO:i:0 XG:i:0 MD:Z:3G1G0G0C1C0C0A0G0C1C0G0G0G0G0C1G1C0G0A1C1T0G0G0T0G0C0G0C0A0G0C0T0C0G0G0G0C2G1C0G1T0G0A0G0G2G0A1C0T0G0C0A0G0C0A0G0C2G1G1T0C0G1T0G0G1T0T0C0C0A0G0G1T0G0G0T0
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 113 supercont1.3762 5 0 100M = 59 54 GATTTGCAACACTCCTGATAAAGAACTTTCCCATTCCGAACCATTGCAAGAGCAGCGAGAGGAAATACAAAATGAATCATGAAAGCGTTTTTGGGGTTAT _Y_YTYTT_XKGTKGb_Zbbcb`_U`^GZZR^Z^GF__\Se_fdfggedgcc^U^U]cc^Xc[geefffegefdY^]bdfgd`Ye_ggcge`cccZc___ XT:A:R NM:i:77 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1C0G0C0C0A0G0T0G0G0C0T0C1A0G0C0G0C0G0G0G1C0T0G0G0C0G0A4G0G0T1C0G1A0G0C1C0G0G0G0C0T1G0C0C0G0A0T5T0G0A0T1T0G0C1G0C1G0C0T0T0G0C0G0C0T0C0G0C1G0G2T0C0C0A0G0G0T1 XA:Z:supercont1.3762,-15,100M,0;supercont1.3762,-135,100M,0;
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 177 supercont1.3762 59 0 100M = 5 -54 TCCTCTCGCTGCTCTTGCAATGGTTCGGAATGGGAAAGTTCTTTATCAGGAGTGTTGCAAATCGGAAGCATTCAAATCCTCAGTGTTTCCACTACTCATG BBBBB_ZTTTZQ_]Ya`_`Z]X]ZYXedc_\R_heeb_\a[eabfe^cZ^_^fea^XcZfdcc^b`b^YQXabdde^ba_]gadfbY^^`Q[a\\\Y^[\ XT:A:R NM:i:68 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C0G0A1G0A0G1A2A3G0C0A0G0C0A1C2G0C1C0T0C1C0T0G0G0T0T1C1A0G0G0T1G0G0T3C0A0G0G0C0G0C1G1T1C0T0C0C0A0G0C0A1G0T0C0G0G0G0C0G0C1A1G3T0G1G0C3G1C0 XA:Z:supercont1.3762,-14,100M,0;supercont1.3762,-6,100M,0;
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 113 supercont1.3762 7 0 100M = 12 5 TTCGACCTTAGTGGTATAATCAAAGTATCCAGGAAAATAATAGTAGTTAAAACAACACAAATACCATACAGTGAACCTTCAAAATATTGGCTATAATTTT BBBb]__ab]_b]d]``Zbddbd]deYchhdge\SWHHddhhfebddhhhgccXYcXbY^Sdehhhhggdfc_Xf`ffhedd__e_hgceaeccccc___ XT:A:R NM:i:81 SM:i:0 AM:i:0 X0:i:12 X1:i:228 XM:i:4 XO:i:0 XG:i:0 MD:Z:0G0C1A0G0T0G0G0C0T0C0C0A1C0G0C0G0G0G0G0C0T0G1C0G0A3T1G0T0G0C0G0C1G0C0T0C0G1G0C0T0G0G0C1G1T0G0A0G0G2G0A0T0C1G3C0A0G0C0T0T0G0C0G0C0T0C0G0C0T0G0G0T0T0T0C0C0A0G0G2G0G0
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 177 supercont1.3762 12 0 100M = 7 -5 TATTTTGAAGGTTCACTGTATGGTATTTGTGTTGTTTTAACTACTATTGTTTTCCTGGATACTTTGATTATACCACTAAGGTCGAACTTTTGCCCCACCT bbb`Ybbbbabb]YTYbbbbb_bb__ba^ddgggeffc_bZ_V__\dbZehgebcggcaaX^dhfe^efc^^_cXhhhhhhfge`J`ggeeeccc`\__^ XT:A:R NM:i:79 SM:i:0 AM:i:0 X0:i:19 X1:i:236 XM:i:3 XO:i:0 XG:i:0 MD:Z:1G0G0C1C0C1G0C1C0G0G0G0G0C0T0G0G0C1A0C0C0A1G3C0G0C0A0G0C1C0G0G0G0C0T0G0G0C0C1A1G0A0G0G0A0T3C0T0G0C0A1C0A0G0C1T0G1G2C0G0C0T0G0G0T0T0T1C0A0G0G0T0T0G0G0T0G0A0G0C0
and the tail of my sam file with unmapped reads removed looks like
FCD1V1KACXX:7:2316:21315:100830#CGATGTA 113 supercont1.3762 16 0 100M = 23 7 TCCCTACGATTTTAATTTCGGTTCCTCAATTCGCCACTTACGTTGATTTCTTATGGAGGGTGGCGAAACAGGAACAGGTGGCGAAAAATAGGTGCAAAGG BBBBB^WYcbb`_`a]Xaaaaa`^]_b_]`bdded^^^Q\afe\V\hgbXe_^Zgeage^Pe^^Xge^[dfbd^bafYefb^]hhgfb[]e``aWcc[__ XT:A:R NM:i:80 SM:i:0 AM:i:0 X0:i:3 X1:i:5 XM:i:2 XO:i:0 XG:i:0 MD:Z:3A0G0C0G0C0G0G0G0G0C0T0G0G0C0G0A0C0C0A1G0G1G0C0G0C0A0G0C0T1G0G0G0C0T0G1C0C3G0A0G0G0A0T0G0A0T0C0T1C0A1C0A1C0T0T0G0C1C0T0C0G0C0T1G0T0T0T0C0C1G0G0T1G1T0G0A0G0C1G1C0 XA:Z:supercont1.3762,-1,100M,2;supercont1.3762,-34,100M,2;supercont1.3762,-81,100M,3;supercont1.3762,-5,100M,3;supercont1.3762,-7,100M,3;supercont1.3762,-4,100M,3;supercont1.3762,-17,100M,3;
FCD1V1KACXX:7:2316:21315:100830#CGATGTA 177 supercont1.3762 23 0 100M = 16 -7 CCATAAGAAATCAACGTAAGTGGCGAATTGAGGAACCGAAATTAAAATCGTGGCGAATACTGGTGCAAGTGGTCCAGTATTCGCCACCATCATTTTTAAT bcccbdcccb^^cccbccbcccaacccbcdddcceeggggefghhihhggfhg`hggaXgfhhihdfhiiihgfbgfhiiihgfb[hgggeeceeec_^_ XT:A:R NM:i:78 SM:i:0 AM:i:0 X0:i:3 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:1G0G0G0G0C0T0G0G0C0G0A0C0C0A0T0G0G0T1C1C0A1C0T0C0G1G0C0T0G0G4T0G0A0G0G1T0G0A0T0C2C0A1C1G0C0T2C0G0C0T0C0G0C4T0T0C0C0A0G0G1T1G0T0G0A0G0C0A0G0G0C0G0C0A0G0T0T0G0 XA:Z:supercont1.3762,-64,100M,0;supercont1.3762,-33,100M,0;supercont1.3762,-35,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 113 supercont1.3762 35 20 100M = 40 5 ACCATGCTGAGATGATCATTCACTTACTTTCAGAGCAACACTGCTTTTTTGCTGTAGAACATAGTAGCCTGGATTACTTTGATCTATTCTATCCACCAGG aaa`_]`Yaa`bc_R_adcaZVZ^\^b]`RddbS_\b\_\_be[de_df_hf]bhhhfea_edbffdee[gdb[c`[d^Y[Sb_dddYb[cWc`Jcc___ XT:A:U NM:i:79 SM:i:20 AM:i:20 X0:i:1 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C1A0T0G1T0G0C0G0C1G0C0T0C0G0G0G0C0T0G0G0C0C0G0A1G0A0G0G0A0T1A0T0C0T0G1A2A0G0C2G0C0G0C0T0C0G0C0T0G0G0T1T0C0C2G0T3T0G0A0G1A0G0G0C0G0C0A0G0T1G2C0C0A0G0C0A1G0T0C0 XA:Z:supercont1.3762,-4,100M,1;supercont1.3762,-16,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 177 supercont1.3762 40 37 100M = 35 -5 GATCAAAGTAATCCAGGCTACTATGTTCTACAGCAAAAAAGCAGTGTTGCTCTGAAAGTAAGTGAATGATCATCTCAGCATGGTTTAGACTTTGTTATTA bbbbc`bbbbb`b`db_c`Yeegggdcegdhhhhhgf`bWddhhheaXOIecfggghhhhhfdf`bfbXfffhffhhhdhghgdffeb[Z^cccaee___ XT:A:U NM:i:79 SM:i:37 AM:i:20 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1T0G1G0C2C0T0C0G0G0G0C0T1G0C0C0G0A0T0G0A0G0G0A1G0A0T0C0T0G0C1G0C3T0T0G0C0G0C0T1G3G0T0T0T0C0C2G0T0T0G0G0T0G0A0G0C0A0G0G1G0C0A0G1T1C1C0C0A0G1A0C0G0T0C0G0G0G0C0G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 113 supercont1.3762 2 7 100M = 8 6 AAACGTTACAATTAATTTTCGACAAAATTGCAATTTTGGGCTTGAACCAAATTAATCATGTAAAAAATTGGCAAAATTGTTACCTTGACTTTCTATTGAC BBBa`b_]``bbbb`XTZZ]adgdb`dbfcgcbe`ge_ZaWbegfaShhhgfhhhehhhefghhhhhfgdfhhhhhhhhhgedfddecgggeaccee__b XT:A:U NM:i:77 SM:i:7 AM:i:7 X0:i:1 X1:i:39 XM:i:0 XO:i:0 XG:i:0 MD:Z:0G0C0T0G0C0G0C0C0A0G0T0G0G0C0T0C0C0A0G2C0G0G0G0G0C1G2G1C0C0A3T0G0C0G0C1G1T0C0G0G0G0C0T0G0G1C0G0A1G1G0G1T0G0A0T0C0T0G0C1G0C0A1C1T0G1G0C0T0C0G0C1G0G1T1C0C1G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 177 supercont1.3762 8 7 100M = 2 -6 CCAATTTTTTACATGATTAATTTGGTTCAAGCCCAAAATTGCAATTTTGTCGAAAATTAATTGTAACGTTTCATTTTCCCCGACCACTGGAAGCATGATG _]_aabbdcb`Y]bbcbbbbaaaabbaa`_`]ac_^Z]_d`degghhgeZfhffhgec[cbbaaZaf_hhhhhhgffgagfhbhhhfgcegecaccc___ XT:A:U NM:i:76 SM:i:7 AM:i:7 X0:i:1 X1:i:38 XM:i:0 XO:i:0 XG:i:0 MD:Z:3G1G0G0C1C0C0A0G0C1C0G0G0G0G0C1G1C0G0A1C1T0G0G0T0G0C0G0C0A0G0C0T0C0G0G0G0C2G1C0G1T0G0A0G0G2G0A1C0T0G0C0A0G0C0A0G0C2G1G1T0C0G1T0G0G1T0T0C0C0A0G0G1T0G0G0T0
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 113 supercont1.3762 5 0 100M = 59 54 GATTTGCAACACTCCTGATAAAGAACTTTCCCATTCCGAACCATTGCAAGAGCAGCGAGAGGAAATACAAAATGAATCATGAAAGCGTTTTTGGGGTTAT _Y_YTYTT_XKGTKGb_Zbbcb`_U`^GZZR^Z^GF__\Se_fdfggedgcc^U^U]cc^Xc[geefffegefdY^]bdfgd`Ye_ggcge`cccZc___ XT:A:R NM:i:77 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1C0G0C0C0A0G0T0G0G0C0T0C1A0G0C0G0C0G0G0G1C0T0G0G0C0G0A4G0G0T1C0G1A0G0C1C0G0G0G0C0T1G0C0C0G0A0T5T0G0A0T1T0G0C1G0C1G0C0T0T0G0C0G0C0T0C0G0C1G0G2T0C0C0A0G0G0T1 XA:Z:supercont1.3762,-15,100M,0;supercont1.3762,-135,100M,0;
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 177 supercont1.3762 59 0 100M = 5 -54 TCCTCTCGCTGCTCTTGCAATGGTTCGGAATGGGAAAGTTCTTTATCAGGAGTGTTGCAAATCGGAAGCATTCAAATCCTCAGTGTTTCCACTACTCATG BBBBB_ZTTTZQ_]Ya`_`Z]X]ZYXedc_\R_heeb_\a[eabfe^cZ^_^fea^XcZfdcc^b`b^YQXabdde^ba_]gadfbY^^`Q[a\\\Y^[\ XT:A:R NM:i:68 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C0G0A1G0A0G1A2A3G0C0A0G0C0A1C2G0C1C0T0C1C0T0G0G0T0T1C1A0G0G0T1G0G0T3C0A0G0G0C0G0C1G1T1C0T0C0C0A0G0C0A1G0T0C0G0G0G0C0G0C1A1G3T0G1G0C3G1C0 XA:Z:supercont1.3762,-14,100M,0;supercont1.3762,-6,100M,0;
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 113 supercont1.3762 7 0 100M = 12 5 TTCGACCTTAGTGGTATAATCAAAGTATCCAGGAAAATAATAGTAGTTAAAACAACACAAATACCATACAGTGAACCTTCAAAATATTGGCTATAATTTT BBBb]__ab]_b]d]``Zbddbd]deYchhdge\SWHHddhhfebddhhhgccXYcXbY^Sdehhhhggdfc_Xf`ffhedd__e_hgceaeccccc___ XT:A:R NM:i:81 SM:i:0 AM:i:0 X0:i:12 X1:i:228 XM:i:4 XO:i:0 XG:i:0 MD:Z:0G0C1A0G0T0G0G0C0T0C0C0A1C0G0C0G0G0G0G0C0T0G1C0G0A3T1G0T0G0C0G0C1G0C0T0C0G1G0C0T0G0G0C1G1T0G0A0G0G2G0A0T0C1G3C0A0G0C0T0T0G0C0G0C0T0C0G0C0T0G0G0T0T0T0C0C0A0G0G2G0G0
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 177 supercont1.3762 12 0 100M = 7 -5 TATTTTGAAGGTTCACTGTATGGTATTTGTGTTGTTTTAACTACTATTGTTTTCCTGGATACTTTGATTATACCACTAAGGTCGAACTTTTGCCCCACCT bbb`Ybbbbabb]YTYbbbbb_bb__ba^ddgggeffc_bZ_V__\dbZehgebcggcaaX^dhfe^efc^^_cXhhhhhhfge`J`ggeeeccc`\__^ XT:A:R NM:i:79 SM:i:0 AM:i:0 X0:i:19 X1:i:236 XM:i:3 XO:i:0 XG:i:0 MD:Z:1G0G0C1C0C1G0C1C0G0G0G0G0C0T0G0G0C1A0C0C0A1G3C0G0C0A0G0C1C0G0G0G0C0T0G0G0C0C1A1G0A0G0G0A0T3C0T0G0C0A1C0A0G0C1T0G1G2C0G0C0T0G0G0T0T0T1C0A0G0G0T0T0G0G0T0G0A0G0C0
the tail of my sam file looks like
CD1V1KACXX:7:2316:21368:100847#NNNNNNN 77 * 0 0 * * 0 0 GATGACGATTTGGACGGAAAACANTATGCTTGCGAGTTAATTNATGTCGAATTGAAATCTATTTCTGGTAGCGAGTCTCTTTTTNNNATTACTGTTGATT [__VcZcZe^aaaX`ddeedeedBPY^P^aae[Yc_OGHHNWBLLT_dZ\dV^`YZZVZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
FCD1V1KACXX:7:2316:21368:100847#NNNNNNN 141 * 0 0 * * 0 0 NTTAACATTTTTAAAGTACTTTAGATNNNNNNCTTAACTCACCANNNNNNNNNCTAAAAANAAACTCTCNACCAGCCCTATATTTNCATTCTNNNNNNNN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 113 supercont1.3762 35 20 100M = 40 5 ACCATGCTGAGATGATCATTCACTTACTTTCAGAGCAACACTGCTTTTTTGCTGTAGAACATAGTAGCCTGGATTACTTTGATCTATTCTATCCACCAGG aaa`_]`Yaa`bc_R_adcaZVZ^\^b]`RddbS_\b\_\_be[de_df_hf]bhhhfea_edbffdee[gdb[c`[d^Y[Sb_dddYb[cWc`Jcc___ XT:A:U NM:i:79 SM:i:20 AM:i:20 X0:i:1 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C1A0T0G1T0G0C0G0C1G0C0T0C0G0G0G0C0T0G0G0C0C0G0A1G0A0G0G0A0T1A0T0C0T0G1A2A0G0C2G0C0G0C0T0C0G0C0T0G0G0T1T0C0C2G0T3T0G0A0G1A0G0G0C0G0C0A0G0T1G2C0C0A0G0C0A1G0T0C0 XA:Z:supercont1.3762,-4,100M,1;supercont1.3762,-16,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 177 supercont1.3762 40 37 100M = 35 -5 GATCAAAGTAATCCAGGCTACTATGTTCTACAGCAAAAAAGCAGTGTTGCTCTGAAAGTAAGTGAATGATCATCTCAGCATGGTTTAGACTTTGTTATTA bbbbc`bbbbb`b`db_c`Yeegggdcegdhhhhhgf`bWddhhheaXOIecfggghhhhhfdf`bfbXfffhffhhhdhghgdffeb[Z^cccaee___ XT:A:U NM:i:79 SM:i:37 AM:i:20 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1T0G1G0C2C0T0C0G0G0G0C0T1G0C0C0G0A0T0G0A0G0G0A1G0A0T0C0T0G0C1G0C3T0T0G0C0G0C0T1G3G0T0T0T0C0C2G0T0T0G0G0T0G0A0G0C0A0G0G1G0C0A0G1T1C1C0C0A0G1A0C0G0T0C0G0G0G0C0G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 113 supercont1.3762 2 7 100M = 8 6 AAACGTTACAATTAATTTTCGACAAAATTGCAATTTTGGGCTTGAACCAAATTAATCATGTAAAAAATTGGCAAAATTGTTACCTTGACTTTCTATTGAC BBBa`b_]``bbbb`XTZZ]adgdb`dbfcgcbe`ge_ZaWbegfaShhhgfhhhehhhefghhhhhfgdfhhhhhhhhhgedfddecgggeaccee__b XT:A:U NM:i:77 SM:i:7 AM:i:7 X0:i:1 X1:i:39 XM:i:0 XO:i:0 XG:i:0 MD:Z:0G0C0T0G0C0G0C0C0A0G0T0G0G0C0T0C0C0A0G2C0G0G0G0G0C1G2G1C0C0A3T0G0C0G0C1G1T0C0G0G0G0C0T0G0G1C0G0A1G1G0G1T0G0A0T0C0T0G0C1G0C0A1C1T0G1G0C0T0C0G0C1G0G1T1C0C1G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 177 supercont1.3762 8 7 100M = 2 -6 CCAATTTTTTACATGATTAATTTGGTTCAAGCCCAAAATTGCAATTTTGTCGAAAATTAATTGTAACGTTTCATTTTCCCCGACCACTGGAAGCATGATG _]_aabbdcb`Y]bbcbbbbaaaabbaa`_`]ac_^Z]_d`degghhgeZfhffhgec[cbbaaZaf_hhhhhhgffgagfhbhhhfgcegecaccc___ XT:A:U NM:i:76 SM:i:7 AM:i:7 X0:i:1 X1:i:38 XM:i:0 XO:i:0 XG:i:0 MD:Z:3G1G0G0C1C0C0A0G0C1C0G0G0G0G0C1G1C0G0A1C1T0G0G0T0G0C0G0C0A0G0C0T0C0G0G0G0C2G1C0G1T0G0A0G0G2G0A1C0T0G0C0A0G0C0A0G0C2G1G1T0C0G1T0G0G1T0T0C0C0A0G0G1T0G0G0T0
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 113 supercont1.3762 5 0 100M = 59 54 GATTTGCAACACTCCTGATAAAGAACTTTCCCATTCCGAACCATTGCAAGAGCAGCGAGAGGAAATACAAAATGAATCATGAAAGCGTTTTTGGGGTTAT _Y_YTYTT_XKGTKGb_Zbbcb`_U`^GZZR^Z^GF__\Se_fdfggedgcc^U^U]cc^Xc[geefffegefdY^]bdfgd`Ye_ggcge`cccZc___ XT:A:R NM:i:77 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1C0G0C0C0A0G0T0G0G0C0T0C1A0G0C0G0C0G0G0G1C0T0G0G0C0G0A4G0G0T1C0G1A0G0C1C0G0G0G0C0T1G0C0C0G0A0T5T0G0A0T1T0G0C1G0C1G0C0T0T0G0C0G0C0T0C0G0C1G0G2T0C0C0A0G0G0T1 XA:Z:supercont1.3762,-15,100M,0;supercont1.3762,-135,100M,0;
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 177 supercont1.3762 59 0 100M = 5 -54 TCCTCTCGCTGCTCTTGCAATGGTTCGGAATGGGAAAGTTCTTTATCAGGAGTGTTGCAAATCGGAAGCATTCAAATCCTCAGTGTTTCCACTACTCATG BBBBB_ZTTTZQ_]Ya`_`Z]X]ZYXedc_\R_heeb_\a[eabfe^cZ^_^fea^XcZfdcc^b`b^YQXabdde^ba_]gadfbY^^`Q[a\\\Y^[\ XT:A:R NM:i:68 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C0G0A1G0A0G1A2A3G0C0A0G0C0A1C2G0C1C0T0C1C0T0G0G0T0T1C1A0G0G0T1G0G0T3C0A0G0G0C0G0C1G1T1C0T0C0C0A0G0C0A1G0T0C0G0G0G0C0G0C1A1G3T0G1G0C3G1C0 XA:Z:supercont1.3762,-14,100M,0;supercont1.3762,-6,100M,0;
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 113 supercont1.3762 7 0 100M = 12 5 TTCGACCTTAGTGGTATAATCAAAGTATCCAGGAAAATAATAGTAGTTAAAACAACACAAATACCATACAGTGAACCTTCAAAATATTGGCTATAATTTT BBBb]__ab]_b]d]``Zbddbd]deYchhdge\SWHHddhhfebddhhhgccXYcXbY^Sdehhhhggdfc_Xf`ffhedd__e_hgceaeccccc___ XT:A:R NM:i:81 SM:i:0 AM:i:0 X0:i:12 X1:i:228 XM:i:4 XO:i:0 XG:i:0 MD:Z:0G0C1A0G0T0G0G0C0T0C0C0A1C0G0C0G0G0G0G0C0T0G1C0G0A3T1G0T0G0C0G0C1G0C0T0C0G1G0C0T0G0G0C1G1T0G0A0G0G2G0A0T0C1G3C0A0G0C0T0T0G0C0G0C0T0C0G0C0T0G0G0T0T0T0C0C0A0G0G2G0G0
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 177 supercont1.3762 12 0 100M = 7 -5 TATTTTGAAGGTTCACTGTATGGTATTTGTGTTGTTTTAACTACTATTGTTTTCCTGGATACTTTGATTATACCACTAAGGTCGAACTTTTGCCCCACCT bbb`Ybbbbabb]YTYbbbbb_bb__ba^ddgggeffc_bZ_V__\dbZehgebcggcaaX^dhfe^efc^^_cXhhhhhhfge`J`ggeeeccc`\__^ XT:A:R NM:i:79 SM:i:0 AM:i:0 X0:i:19 X1:i:236 XM:i:3 XO:i:0 XG:i:0 MD:Z:1G0G0C1C0C1G0C1C0G0G0G0G0C0T0G0G0C1A0C0C0A1G3C0G0C0A0G0C1C0G0G0G0C0T0G0G0C0C1A1G0A0G0G0A0T3C0T0G0C0A1C0A0G0C1T0G1G2C0G0C0T0G0G0T0T0T1C0A0G0G0T0T0G0G0T0G0A0G0C0
and the tail of my sam file with unmapped reads removed looks like
FCD1V1KACXX:7:2316:21315:100830#CGATGTA 113 supercont1.3762 16 0 100M = 23 7 TCCCTACGATTTTAATTTCGGTTCCTCAATTCGCCACTTACGTTGATTTCTTATGGAGGGTGGCGAAACAGGAACAGGTGGCGAAAAATAGGTGCAAAGG BBBBB^WYcbb`_`a]Xaaaaa`^]_b_]`bdded^^^Q\afe\V\hgbXe_^Zgeage^Pe^^Xge^[dfbd^bafYefb^]hhgfb[]e``aWcc[__ XT:A:R NM:i:80 SM:i:0 AM:i:0 X0:i:3 X1:i:5 XM:i:2 XO:i:0 XG:i:0 MD:Z:3A0G0C0G0C0G0G0G0G0C0T0G0G0C0G0A0C0C0A1G0G1G0C0G0C0A0G0C0T1G0G0G0C0T0G1C0C3G0A0G0G0A0T0G0A0T0C0T1C0A1C0A1C0T0T0G0C1C0T0C0G0C0T1G0T0T0T0C0C1G0G0T1G1T0G0A0G0C1G1C0 XA:Z:supercont1.3762,-1,100M,2;supercont1.3762,-34,100M,2;supercont1.3762,-81,100M,3;supercont1.3762,-5,100M,3;supercont1.3762,-7,100M,3;supercont1.3762,-4,100M,3;supercont1.3762,-17,100M,3;
FCD1V1KACXX:7:2316:21315:100830#CGATGTA 177 supercont1.3762 23 0 100M = 16 -7 CCATAAGAAATCAACGTAAGTGGCGAATTGAGGAACCGAAATTAAAATCGTGGCGAATACTGGTGCAAGTGGTCCAGTATTCGCCACCATCATTTTTAAT bcccbdcccb^^cccbccbcccaacccbcdddcceeggggefghhihhggfhg`hggaXgfhhihdfhiiihgfbgfhiiihgfb[hgggeeceeec_^_ XT:A:R NM:i:78 SM:i:0 AM:i:0 X0:i:3 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:1G0G0G0G0C0T0G0G0C0G0A0C0C0A0T0G0G0T1C1C0A1C0T0C0G1G0C0T0G0G4T0G0A0G0G1T0G0A0T0C2C0A1C1G0C0T2C0G0C0T0C0G0C4T0T0C0C0A0G0G1T1G0T0G0A0G0C0A0G0G0C0G0C0A0G0T0T0G0 XA:Z:supercont1.3762,-64,100M,0;supercont1.3762,-33,100M,0;supercont1.3762,-35,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 113 supercont1.3762 35 20 100M = 40 5 ACCATGCTGAGATGATCATTCACTTACTTTCAGAGCAACACTGCTTTTTTGCTGTAGAACATAGTAGCCTGGATTACTTTGATCTATTCTATCCACCAGG aaa`_]`Yaa`bc_R_adcaZVZ^\^b]`RddbS_\b\_\_be[de_df_hf]bhhhfea_edbffdee[gdb[c`[d^Y[Sb_dddYb[cWc`Jcc___ XT:A:U NM:i:79 SM:i:20 AM:i:20 X0:i:1 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C1A0T0G1T0G0C0G0C1G0C0T0C0G0G0G0C0T0G0G0C0C0G0A1G0A0G0G0A0T1A0T0C0T0G1A2A0G0C2G0C0G0C0T0C0G0C0T0G0G0T1T0C0C2G0T3T0G0A0G1A0G0G0C0G0C0A0G0T1G2C0C0A0G0C0A1G0T0C0 XA:Z:supercont1.3762,-4,100M,1;supercont1.3762,-16,100M,1;
FCD1V1KACXX:7:2316:21336:100849#CTATGTA 177 supercont1.3762 40 37 100M = 35 -5 GATCAAAGTAATCCAGGCTACTATGTTCTACAGCAAAAAAGCAGTGTTGCTCTGAAAGTAAGTGAATGATCATCTCAGCATGGTTTAGACTTTGTTATTA bbbbc`bbbbb`b`db_c`Yeegggdcegdhhhhhgf`bWddhhheaXOIecfggghhhhhfdf`bfbXfffhffhhhdhghgdffeb[Z^cccaee___ XT:A:U NM:i:79 SM:i:37 AM:i:20 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1T0G1G0C2C0T0C0G0G0G0C0T1G0C0C0G0A0T0G0A0G0G0A1G0A0T0C0T0G0C1G0C3T0T0G0C0G0C0T1G3G0T0T0T0C0C2G0T0T0G0G0T0G0A0G0C0A0G0G1G0C0A0G1T1C1C0C0A0G1A0C0G0T0C0G0G0G0C0G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 113 supercont1.3762 2 7 100M = 8 6 AAACGTTACAATTAATTTTCGACAAAATTGCAATTTTGGGCTTGAACCAAATTAATCATGTAAAAAATTGGCAAAATTGTTACCTTGACTTTCTATTGAC BBBa`b_]``bbbb`XTZZ]adgdb`dbfcgcbe`ge_ZaWbegfaShhhgfhhhehhhefghhhhhfgdfhhhhhhhhhgedfddecgggeaccee__b XT:A:U NM:i:77 SM:i:7 AM:i:7 X0:i:1 X1:i:39 XM:i:0 XO:i:0 XG:i:0 MD:Z:0G0C0T0G0C0G0C0C0A0G0T0G0G0C0T0C0C0A0G2C0G0G0G0G0C1G2G1C0C0A3T0G0C0G0C1G1T0C0G0G0G0C0T0G0G1C0G0A1G1G0G1T0G0A0T0C0T0G0C1G0C0A1C1T0G1G0C0T0C0G0C1G0G1T1C0C1G0
FCD1V1KACXX:7:2316:21278:100873#CGATGTA 177 supercont1.3762 8 7 100M = 2 -6 CCAATTTTTTACATGATTAATTTGGTTCAAGCCCAAAATTGCAATTTTGTCGAAAATTAATTGTAACGTTTCATTTTCCCCGACCACTGGAAGCATGATG _]_aabbdcb`Y]bbcbbbbaaaabbaa`_`]ac_^Z]_d`degghhgeZfhffhgec[cbbaaZaf_hhhhhhgffgagfhbhhhfgcegecaccc___ XT:A:U NM:i:76 SM:i:7 AM:i:7 X0:i:1 X1:i:38 XM:i:0 XO:i:0 XG:i:0 MD:Z:3G1G0G0C1C0C0A0G0C1C0G0G0G0G0C1G1C0G0A1C1T0G0G0T0G0C0G0C0A0G0C0T0C0G0G0G0C2G1C0G1T0G0A0G0G2G0A1C0T0G0C0A0G0C0A0G0C2G1G1T0C0G1T0G0G1T0T0C0C0A0G0G1T0G0G0T0
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 113 supercont1.3762 5 0 100M = 59 54 GATTTGCAACACTCCTGATAAAGAACTTTCCCATTCCGAACCATTGCAAGAGCAGCGAGAGGAAATACAAAATGAATCATGAAAGCGTTTTTGGGGTTAT _Y_YTYTT_XKGTKGb_Zbbcb`_U`^GZZR^Z^GF__\Se_fdfggedgcc^U^U]cc^Xc[geefffegefdY^]bdfgd`Ye_ggcge`cccZc___ XT:A:R NM:i:77 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:1C0G0C0C0A0G0T0G0G0C0T0C1A0G0C0G0C0G0G0G1C0T0G0G0C0G0A4G0G0T1C0G1A0G0C1C0G0G0G0C0T1G0C0C0G0A0T5T0G0A0T1T0G0C1G0C1G0C0T0T0G0C0G0C0T0C0G0C1G0G2T0C0C0A0G0G0T1 XA:Z:supercont1.3762,-15,100M,0;supercont1.3762,-135,100M,0;
FCD1V1KACXX:7:2316:21259:100897#CGATGTA 177 supercont1.3762 59 0 100M = 5 -54 TCCTCTCGCTGCTCTTGCAATGGTTCGGAATGGGAAAGTTCTTTATCAGGAGTGTTGCAAATCGGAAGCATTCAAATCCTCAGTGTTTCCACTACTCATG BBBBB_ZTTTZQ_]Ya`_`Z]X]ZYXedc_\R_heeb_\a[eabfe^cZ^_^fea^XcZfdcc^b`b^YQXabdde^ba_]gadfbY^^`Q[a\\\Y^[\ XT:A:R NM:i:68 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:0C0G0A1G0A0G1A2A3G0C0A0G0C0A1C2G0C1C0T0C1C0T0G0G0T0T1C1A0G0G0T1G0G0T3C0A0G0G0C0G0C1G1T1C0T0C0C0A0G0C0A1G0T0C0G0G0G0C0G0C1A1G3T0G1G0C3G1C0 XA:Z:supercont1.3762,-14,100M,0;supercont1.3762,-6,100M,0;
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 113 supercont1.3762 7 0 100M = 12 5 TTCGACCTTAGTGGTATAATCAAAGTATCCAGGAAAATAATAGTAGTTAAAACAACACAAATACCATACAGTGAACCTTCAAAATATTGGCTATAATTTT BBBb]__ab]_b]d]``Zbddbd]deYchhdge\SWHHddhhfebddhhhgccXYcXbY^Sdehhhhggdfc_Xf`ffhedd__e_hgceaeccccc___ XT:A:R NM:i:81 SM:i:0 AM:i:0 X0:i:12 X1:i:228 XM:i:4 XO:i:0 XG:i:0 MD:Z:0G0C1A0G0T0G0G0C0T0C0C0A1C0G0C0G0G0G0G0C0T0G1C0G0A3T1G0T0G0C0G0C1G0C0T0C0G1G0C0T0G0G0C1G1T0G0A0G0G2G0A0T0C1G3C0A0G0C0T0T0G0C0G0C0T0C0G0C0T0G0G0T0T0T0C0C0A0G0G2G0G0
FCD1V1KACXX:7:2316:21271:100923#CGNNNNA 177 supercont1.3762 12 0 100M = 7 -5 TATTTTGAAGGTTCACTGTATGGTATTTGTGTTGTTTTAACTACTATTGTTTTCCTGGATACTTTGATTATACCACTAAGGTCGAACTTTTGCCCCACCT bbb`Ybbbbabb]YTYbbbbb_bb__ba^ddgggeffc_bZ_V__\dbZehgebcggcaaX^dhfe^efc^^_cXhhhhhhfge`J`ggeeeccc`\__^ XT:A:R NM:i:79 SM:i:0 AM:i:0 X0:i:19 X1:i:236 XM:i:3 XO:i:0 XG:i:0 MD:Z:1G0G0C1C0C1G0C1C0G0G0G0G0C0T0G0G0C1A0C0C0A1G3C0G0C0A0G0C1C0G0G0G0C0T0G0G0C0C1A1G0A0G0G0A0T3C0T0G0C0A1C0A0G0C1T0G1G2C0G0C0T0G0G0T0T0T1C0A0G0G0T0T0G0G0T0G0A0G0C0
Tao Liu
Jun 20, 2014, 12:48:01 PM6/20/14
to macs-ann...@googlegroups.com
Hi Joseph,
The first error means the bam file can't be opened by gzip module in Python. Is it a default compressed version of bam file? Could you check it with samtools flagstat?
Second one may be due to unmapped reads records at the beginning part of Sam file. You can try to assign tag size in command line to bypass auto tag size detection.
Tao
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Joseph Sarro
Jun 20, 2014, 2:16:39 PM6/20/14
to macs-ann...@googlegroups.com
Hi Tao,
Thank you for the reply. I have printed the output of flagstat below. For the SAM files I just tried using the -s option and it did not print out the error this time! However I am a little confused on what the tag size should be. I assume this is not referring to the tags at the begging of the sam file such as @SQ. I picked 100, to test the command with this option, as 100 was the length of the reads before trimming. I am sure this is not what the tage size refers to though. Is there a simple way to figure this out?
Thanks,
Joe-
203646666 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
203646666 + 0 mapped (100.00%:-nan%)
203646666 + 0 paired in sequencing
103754326 + 0 read1
99892340 + 0 read2
14 + 0 properly paired (0.00%:-nan%)
175893682 + 0 with itself and mate mapped
27752984 + 0 singletons (13.63%:-nan%)
557499 + 0 with mate mapped to a different chr
318431 + 0 with mate mapped to a different chr (mapQ>=5)
Thank you for the reply. I have printed the output of flagstat below. For the SAM files I just tried using the -s option and it did not print out the error this time! However I am a little confused on what the tag size should be. I assume this is not referring to the tags at the begging of the sam file such as @SQ. I picked 100, to test the command with this option, as 100 was the length of the reads before trimming. I am sure this is not what the tage size refers to though. Is there a simple way to figure this out?
Thanks,
Joe-
203646666 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
203646666 + 0 mapped (100.00%:-nan%)
203646666 + 0 paired in sequencing
103754326 + 0 read1
99892340 + 0 read2
14 + 0 properly paired (0.00%:-nan%)
175893682 + 0 with itself and mate mapped
27752984 + 0 singletons (13.63%:-nan%)
557499 + 0 with mate mapped to a different chr
318431 + 0 with mate mapped to a different chr (mapQ>=5)
Tao Liu
Jun 20, 2014, 2:53:40 PM6/20/14
to macs-ann...@googlegroups.com
Hi Joe,
According to the last few lines for mapped reads of your SAM file, the tag size should be 100. You can see CIGAR string ‘100M’ there which means 100bps read can be totally aligned to the genome. However, I am not sure whether your alignment results are good or not. The ‘MD:Z’ tags show a lot of mismatches.
I suggest you remove some ( perhaps hundreds of small supercontigs) then redo the alignment. Otherwise your data contains too much noise. See only 14 reads are paired? If you let MACS2 process such data, only the ‘paired’ ones will be kept...
Best,
Tao
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