Error during Runchicago.R

[XianglongTan]

Hi I’ve been using the following code to run Chicago program:

Rscript /media/data/Xianglongtan/pcHiC/CHICAGO/chicagoTeam-chicago-91a04862d032/chicagoTools/runChicago.R --design-dir /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/ --cutoff 5 --export-format interBed,washU_text /media/data/Xianglongtan/pcHiC/20200817_A549_B2B/Xianglong5384/A1/A1_Chicago/GroupA1/GroupA1.chinput Chicago_outputA1_MboI_cutoff5

But it generates an error during the “** Running estimateTechnicalNoise...“ step, could you please help me solved this issue? The full running log is as follows:

• **runChicago.R

Loading the Chicago package and dependencies...

Loading required package: data.table

Welcome to CHiCAGO - version 1.16.0

If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").

NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")

Warning: neither --en-feat-files nor --en-feat-list provided. Feature enrichments will not be computed

Setting the experiment...

Locating <baitmapfile>.baitmap in /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/...

Found Digest_hg_38_MboI_None_18-28-47_19-05-2020.baitmap

Locating <rmapfile>.rmap in /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/...

Found Digest_hg_38_MboI_None_18-28-47_19-05-2020.rmap

Locating <nperbinfile>.npb in /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/...

Found Digest_hg_38_MboI_None_18-28-47_19-05-2020.npb

Locating <nbaitsperbinfile>.nbpb in /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/...

Found Digest_hg_38_MboI_None_18-28-47_19-05-2020.nbpb

Locating <proxOEfile>.poe in /media/data/Xianglongtan/pcHiC/CHICAGO/MboI/...

Found Digest_hg_38_MboI_None_18-28-47_19-05-2020.poe

Checking the design files...

Reading the settings from NPB file header...

Amending the default maxFragLen setting from 150 to 75 specified in .npb file header.

Amending the default maxFragLen setting from 40000 to 1200 specified in .npb file header.

Amending the default maxLBrownEst setting from 1500000 to 750000 specified in .npb file header.

Amending the default binsize setting from 20000 to 1500 specified in .npb file header.

Reading /media/data/Xianglongtan/pcHiC/20200817_A549_B2B/Xianglong5384/A1/A1_Chicago/GroupA1/GroupA1.chinput

Processing input...

minFragLen = 75 maxFragLen = 1200

Filtered out 511792 interactions involving other ends < minFragLen or > maxFragLen.

minNPerBait = 250

Filtered out 125 baits with < minNPerBait reads.

Removed interactions with fragments adjacent to baits.

Filtered out 0 baits without proximal non-Bait2bait interactions

Starting chicagoPipeline...

• ** Running normaliseBaits...

Normalising baits...

Reading NPerBin file...

Computing binwise means...

• ** Running normaliseOtherEnds...

Preprocessing input...

Computing trans-counts...

Filtering out 92 other ends with top 0.01% number of trans-interactions

Binning...

Computing total bait counts...

Reading NBaitsPerBin file...

Computing scaling factors...

Computing binwise means...

Computing normalised counts...

Post-processing...

• ** Running estimateTechnicalNoise...

Estimating technical noise based on trans-counts...

Binning baits based on observed trans-counts...

Defining interaction pools and gathering the observed numbers of trans-counts per pool...

Computing the total number of possible interactions per pool...

Preparing the data.....

Processing fragment pools..Error in `[.data.table`(cd@x, , { : 

Column 1 of result for group 2 is type 'integer' but expecting type 'double'. Column types must be consistent for each group.

Calls: chicagoPipeline -> estimateTechnicalNoise -> [ -> [.data.table

Execution halted

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