MACS2: Too few paired peaks (0) so I can not build the model!

[dannyjwan]

Description of the bug

Hello,

While running the pipeline, it is encountering issues when running MACS2. Here are the specifics:

-[nf-core/chipseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK (WT_HRCA_IP_REP1)'

Caused by:
Process NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK (WT_HRCA_IP_REP1) terminated with an error exit status (1)

Command executed:

macs2
callpeak
--keep-dup all --broad --broad-cutoff 0.1
--gsize 1000000
--format BAM
--name WT_HRCA_IP_REP1
--treatment WT_HRCA_IP_REP1.mLb.clN.sorted.bam
--control WT_INPUT_REP1.mLb.clN.sorted.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK":
macs2: $(macs2 --version | sed -e "s/macs2 //g")
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
INFO @ Thu, 14 Dec 2023 23:22:41:

Command line: callpeak --keep-dup all --broad --broad-cutoff 0.1 --gsize 1000000 --format BAM --name WT_HRCA_IP_REP1 --treatment WT_HRCA_IP_REP1.mLb.clN.sorted.bam --control WT_INPUT_REP1.mLb.clN.sorted.bam

ARGUMENTS LIST:

name = WT_HRCA_IP_REP1

format = BAM

ChIP-seq file = ['WT_HRCA_IP_REP1.mLb.clN.sorted.bam']

control file = ['WT_INPUT_REP1.mLb.clN.sorted.bam']

effective genome size = 1.00e+06

band width = 300

model fold = [5, 50]

qvalue cutoff for narrow/strong regions = 5.00e-02

qvalue cutoff for broad/weak regions = 1.00e-01

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 on

Paired-End mode is off

INFO @ Thu, 14 Dec 2023 23:22:41: #1 read tag files...
INFO @ Thu, 14 Dec 2023 23:22:41: #1 read treatment tags...
INFO @ Thu, 14 Dec 2023 23:22:43: 1000000
INFO @ Thu, 14 Dec 2023 23:22:44: 1702472 reads have been read.
INFO @ Thu, 14 Dec 2023 23:22:44: #1.2 read input tags...
INFO @ Thu, 14 Dec 2023 23:22:45: 1000000
INFO @ Thu, 14 Dec 2023 23:22:46: 1729564 reads have been read.
INFO @ Thu, 14 Dec 2023 23:22:46: #1 tag size is determined as 40 bps
INFO @ Thu, 14 Dec 2023 23:22:46: #1 tag size = 40.0
INFO @ Thu, 14 Dec 2023 23:22:46: #1 total tags in treatment: 1702472
INFO @ Thu, 14 Dec 2023 23:22:46: #1 total tags in control: 1729564
INFO @ Thu, 14 Dec 2023 23:22:46: #1 finished!
INFO @ Thu, 14 Dec 2023 23:22:46: #2 Build Peak Model...
INFO @ Thu, 14 Dec 2023 23:22:46: #2 looking for paired plus/minus strand peaks...
INFO @ Thu, 14 Dec 2023 23:22:46: #2 number of paired peaks: 0
WARNING @ Thu, 14 Dec 2023 23:22:46: 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 @ Thu, 14 Dec 2023 23:22:46: Process for pairing-model is terminated!

I believe this might be an issue because I am using a bacterial genome and other users on the MACS2 GitHub have reported similar problems (macs3-project/MACS#390).

I was wondering what is the best way to resolve this issue? Thanks!

Command used and terminal output

No response

Relevant files

No response

System information

No response

[JoseEspinosa]

Sorry for the late response, probably not useful to you anymore but in case someone in the future finds this issue, you could provide the --nomodel and --extsize 147 arguments to macs2 as suggested in the tool message. See this answer in nf-core slack.

[JoseEspinosa]

I will close this issue now for lack of activity, if you have any further questions please feel free to re-open it.