Entering edit mode
3.4 years ago
Kai_Qi
▴
130
Hi world:
I am trying to analyze eCLIP-seq data and my PI advised me to call peaks using MACS2. I read the manual on how macs2 can be used for peak calling when doing chip-seq. It looks easy to follow: I just need to provide the macs command bam files. So, I did the following:
$ macs2 callpeak -t GRCh37SRR5111379Aligned.sortedByCoord.out.bam -c GRCh37SRR5111939Aligned.sortedByCoord.out.bam -f BAM -g 1.3e+8 -n HNRNPKRep1 --outdir macs2/ >log1 2>error1
But I got error like this:
INFO @ Sat, 21 Nov 2020 14:51:08:
# Command line: callpeak -t GRCh37SRR5111379Aligned.sortedByCoord.out.bam -c GRCh37SRR5111939Aligned.sortedByCoord.out.bam -f BAM -g 1.3e+8 -n HNRNPKRep1 --outdir macs2/
# ARGUMENTS LIST:
# name = HNRNPKRep1
# format = BAM
# ChIP-seq file = ['GRCh37SRR5111379Aligned.sortedByCoord.out.bam']
# control file = ['GRCh37SRR5111939Aligned.sortedByCoord.out.bam']
# effective genome size = 1.30e+08
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Paired-End mode is off
INFO @ Sat, 21 Nov 2020 14:51:08: #1 read tag files...
INFO @ Sat, 21 Nov 2020 14:51:08: #1 read treatment tags...
INFO @ Sat, 21 Nov 2020 14:51:11: 1000000
INFO @ Sat, 21 Nov 2020 14:51:14: 2000000
INFO @ Sat, 21 Nov 2020 14:51:17: 3000000
INFO @ Sat, 21 Nov 2020 14:51:20: 4000000
INFO @ Sat, 21 Nov 2020 14:51:23: 5000000
INFO @ Sat, 21 Nov 2020 14:51:24: #1.2 read input tags...
INFO @ Sat, 21 Nov 2020 14:51:27: 1000000
INFO @ Sat, 21 Nov 2020 14:51:29: 2000000
INFO @ Sat, 21 Nov 2020 14:51:32: 3000000
INFO @ Sat, 21 Nov 2020 14:51:34: 4000000
INFO @ Sat, 21 Nov 2020 14:51:37: 5000000
INFO @ Sat, 21 Nov 2020 14:51:40: 6000000
INFO @ Sat, 21 Nov 2020 14:51:43: 7000000
INFO @ Sat, 21 Nov 2020 14:51:46: 8000000
INFO @ Sat, 21 Nov 2020 14:51:49: 9000000
INFO @ Sat, 21 Nov 2020 14:51:52: 10000000
INFO @ Sat, 21 Nov 2020 14:51:55: 11000000
INFO @ Sat, 21 Nov 2020 14:51:58: #1 tag size is determined as 42 bps
INFO @ Sat, 21 Nov 2020 14:51:58: #1 tag size = 42.0
INFO @ Sat, 21 Nov 2020 14:51:58: #1 total tags in treatment: 1942896
INFO @ Sat, 21 Nov 2020 14:51:58: #1 user defined the maximum tags...
INFO @ Sat, 21 Nov 2020 14:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Sat, 21 Nov 2020 14:51:58: #1 tags after filtering in treatment: 1617769
INFO @ Sat, 21 Nov 2020 14:51:58: #1 Redundant rate of treatment: 0.17
INFO @ Sat, 21 Nov 2020 14:51:58: #1 total tags in control: 3284905
INFO @ Sat, 21 Nov 2020 14:51:58: #1 user defined the maximum tags...
INFO @ Sat, 21 Nov 2020 14:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Sat, 21 Nov 2020 14:51:58: #1 tags after filtering in control: 1846916
INFO @ Sat, 21 Nov 2020 14:51:58: #1 Redundant rate of control: 0.44
INFO @ Sat, 21 Nov 2020 14:51:58: #1 finished!
INFO @ Sat, 21 Nov 2020 14:51:58: #2 Build Peak Model...
INFO @ Sat, 21 Nov 2020 14:51:58: #2 looking for paired plus/minus strand peaks...
INFO @ Sat, 21 Nov 2020 14:51:58: #2 number of paired peaks: 2
WARNING @ Sat, 21 Nov 2020 14:51:58: Too few paired peaks (2) 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 @ Sat, 21 Nov 2020 14:51:58: Process for pairing-model is terminated!
Does any one can help me correct the command to make it work ?
(This question has been posted here as well: https://github.com/macs3-project/MACS/issues/423)
Thanks,
I got an answer here, in case it will help someone who is looking for help like me: https://github.com/macs3-project/MACS/issues/423