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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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"error in evaluating the argument 'object' in selecting a method for function 'summary': missing value where TRUE/FALSE needed" #92

Open Moonriver1988 opened 3 years ago

Moonriver1988 commented 3 years ago

Hello,

I got the following error, and I cannot find .mango file in the output folder. Could you help me with this? Thank you!

$ hichipper --out raw-1h-rep1_out_hichipper --macs2-genome mm -mu config.yaml
Mon Oct 18 12:24:31 EDT 2021: Starting hichipper pipeline v0.7.5 Mon Oct 18 12:24:31 EDT 2021: Parsing user parameters Mon Oct 18 12:24:31 EDT 2021: .yaml file detected WARNING: While bind mounting '/gs10:/gs10': destination is already in the mount point list Mon Oct 18 12:52:43 EDT 2021: Performing hichipper-modified background peak calling Taking input= as a system command ('zcat < /data/xieb2/H3K27ac-enhancer/H3K27ac_HICHIP/mm9_MboI_resfrag.bed.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Mon Oct 18 13:27:46 EDT 2021: Modified background signal; performing peak calling Mon Oct 18 13:27:46 EDT 2021: MACS2 TEXT OUTPUT INCOMING WARNING: While bind mounting '/gs10:/gs10': destination is already in the mount point list INFO @ Mon, 18 Oct 2021 13:27:47: Read and build treatment bedGraph... INFO @ Mon, 18 Oct 2021 13:33:44: Read and build control bedGraph... INFO @ Mon, 18 Oct 2021 13:35:15: Build scoreTrackII... INFO @ Mon, 18 Oct 2021 13:37:51: Calculate scores comparing treatment and control by 'qpois'... INFO @ Mon, 18 Oct 2021 13:53:40: Write bedGraph of scores... INFO @ Mon, 18 Oct 2021 13:56:07: Finished 'qpois'! Please check 'raw-1h-rep1_out_hichipper/hichipper_qvalue.bdg.tmp'! WARNING: While bind mounting '/gs10:/gs10': destination is already in the mount point list INFO @ Mon, 18 Oct 2021 13:56:10: Read and build bedGraph... INFO @ Mon, 18 Oct 2021 13:57:40: Call peaks from bedGraph... INFO @ Mon, 18 Oct 2021 13:57:49: Write peaks... INFO @ Mon, 18 Oct 2021 13:57:49: Done Taking input= as a system command ('zcat < /data/xieb2/H3K27ac-enhancer/H3K27ac_HICHIP/mm9_MboI_resfrag.bed.gz') and a variable has been used in the expression passed to input=. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Anchors removed due to excessive size (likely at ends of chromosomes): 24 Mon Oct 18 13:58:06 EDT 2021: Processing 1-HiChIP_1hr_H3K27ac Mon Oct 18 13:58:06 EDT 2021: Total_PETs=142631900 Mon Oct 18 13:58:14 EDT 2021: Mapped_unique_quality_pairs=94588373 Mon Oct 18 13:58:14 EDT 2021: Mapped_unique_quality_valid_pairs=4670442 Mon Oct 18 13:58:14 EDT 2021: Intersecting PETs with anchors Mon Oct 18 13:58:14 EDT 2021: Finished the anchor merging. Mon Oct 18 14:17:12 EDT 2021: Intrachromosomal_valid_small=3252710 Mon Oct 18 14:17:19 EDT 2021: Intrachromosomal_valid_med=507490 Mon Oct 18 14:17:25 EDT 2021: Intrachromosomal_valid_large=388083 Mon Oct 18 14:17:25 EDT 2021: Total number of anchors used: 103527 Mon Oct 18 14:17:25 EDT 2021: Total number of reads in anchors: 36810302 Mon Oct 18 14:18:12 EDT 2021: Mapped_unique_intra_quality_anchor=999213 Mon Oct 18 14:18:12 EDT 2021: Mapped_unique_intra_quality_anchor_small=928746 Mon Oct 18 14:18:12 EDT 2021: Mapped_unique_intra_quality_anchor_med=47940 Mon Oct 18 14:18:12 EDT 2021: Mapped_unique_intra_quality_anchor_large=22528 Mon Oct 18 14:18:12 EDT 2021: Creating UCSC Compatible files; make sure tabix and bgzip are available in the environment or this will not work. Mon Oct 18 14:18:13 EDT 2021: Loop_PETs=47940 Mon Oct 18 14:18:13 EDT 2021: ['/usr/local/apps/R/4.1/4.1.0/bin/Rscript', u'raw-1h-rep1_out_hichipper/qcReport.R', '/usr/local/Anaconda/envs_app/hichipper/0.7.5/lib/python2.7/site-packages/hichipper', 'raw-1h-rep1_out_hichipper', '/lscratch/25247087', '0.7.5', '1-HiChIP_1hr_H3K27ac'] /lscratch/25247087Using count as value column: use value.var to override. Processing: 1-HiChIP_1hr_H3K27ac Error in { : task 1 failed - "error in evaluating the argument 'object' in selecting a method for function 'summary': missing value where TRUE/FALSE needed" Calls: %do% -> In addition: There were 38 warnings (use warnings() to see them) Execution halted

Gemma-Zhang-326 commented 3 years ago

Hi, I encountered the same error, did you solve this problem yet? Thanks a lot

Moonriver1988 commented 3 years ago

Hi Gemma, I haven't solve this problem, I think probably is because the data is too sparse(https://github.com/aryeelab/hichipper/issues/16). The test dataset runs well, I got .mango file with test dataset. I am ongoing to re-analyze a high quality published dataset to further test.

Gemma-Zhang-326 commented 3 years ago

Hi Gemma, I haven't solve this problem, I think probably is because the data is too sparse(#16). The test dataset runs well, I got .mango file with test dataset. I am ongoing to re-analyze a high quality published dataset to further test.

Hi, Thank you for reply. Maybe you can try to adjust the -pp --peak-pad parameter to 1000. I tried and it works Hope you succeed.