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nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
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MACS2: Too few paired peaks (0) so I can not build the model! #374

Open dannyjwan opened 6 months ago

dannyjwan commented 6 months ago

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 (https://github.com/macs3-project/MACS/issues/390).

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

Command used and terminal output

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Relevant files

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System information

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