Error in { : task 1 failed - "need at least four unique 'x' values" ; Calls: %do% -> <Anonymous>

[vidaletal]

I'm receiving the following error and I have no idea now where it is coming from

Error in { : task 1 failed - "need at least four unique 'x' values"
Calls: %do% -> <Anonymous>
Execution halted

I'm running the following command:

hichipper --out HiChIPper_full --make-ucsc config.yaml

with this .yaml:

peaks:
- COMBINED,SELF
resfrags:
- DpnII_resfrag_hg19.bed
hicpro_output:
- HiCPro_analysis

This is the stderr:

home:~/Desktop/Software/HiChipper$ hichipper --out HiChIPper_full --make-ucsc config.yaml
Thu Oct 11 18:21:07 CEST 2018: Starting hichipper pipeline v0.7.3
Thu Oct 11 18:21:07 CEST 2018: Parsing user parameters
Thu Oct 11 18:21:07 CEST 2018: .yaml file detected
Thu Oct 11 18:21:11 CEST 2018: Performing hichipper-modified background peak calling
Thu Oct 11 18:23:39 CEST 2018: Modified background signal; performing peak calling
Thu Oct 11 18:23:39 CEST 2018: MACS2 TEXT OUTPUT INCOMING
INFO  @ Thu, 11 Oct 2018 18:23:40: Read and build treatment bedGraph... 
INFO  @ Thu, 11 Oct 2018 18:23:40: Read and build control bedGraph... 
INFO  @ Thu, 11 Oct 2018 18:23:40: Build scoreTrackII... 
INFO  @ Thu, 11 Oct 2018 18:23:41: Calculate scores comparing treatment and control by 'qpois'... 
INFO  @ Thu, 11 Oct 2018 18:23:41: Write bedGraph of scores... 
INFO  @ Thu, 11 Oct 2018 18:23:42: Finished 'qpois'! Please check 'HiChIPper_full/hichipper_qvalue.bdg.tmp'! 
INFO  @ Thu, 11 Oct 2018 18:23:42: Read and build bedGraph... 
INFO  @ Thu, 11 Oct 2018 18:23:42: Call peaks from bedGraph... 
INFO  @ Thu, 11 Oct 2018 18:23:42: Write peaks... 
INFO  @ Thu, 11 Oct 2018 18:23:42: Done 
Anchors removed due to excessive size (likely at ends of chromosomes): 3 
Do 11. Okt 18:24:42 CEST 2018: Processing HiChIP
Do 11. Okt 18:24:42 CEST 2018: Total_PETs=820685
Do 11. Okt 18:24:42 CEST 2018: Mapped_unique_quality_pairs=473801
Do 11. Okt 18:24:42 CEST 2018: Mapped_unique_quality_valid_pairs=127230
Do 11. Okt 18:24:42 CEST 2018: Intersecting PETs with anchors
Do 11. Okt 18:24:42 CEST 2018: Finished the anchor merging.
Do 11. Okt 18:24:46 CEST 2018: Intrachromosomal_valid_small=33568
Do 11. Okt 18:24:46 CEST 2018: Intrachromosomal_valid_med=71004
Do 11. Okt 18:24:47 CEST 2018: Intrachromosomal_valid_large=10097
Do 11. Okt 18:24:47 CEST 2018: Total number of anchors used: 9635
Do 11. Okt 18:24:47 CEST 2018: Total number of reads in anchors: 98023
Do 11. Okt 18:24:47 CEST 2018: Mapped_unique_intra_quality_anchor=839
Do 11. Okt 18:24:47 CEST 2018: Mapped_unique_intra_quality_anchor_small=779
Do 11. Okt 18:24:47 CEST 2018: Mapped_unique_intra_quality_anchor_med=59
Do 11. Okt 18:24:47 CEST 2018: Mapped_unique_intra_quality_anchor_large=1
Do 11. Okt 18:24:47 CEST 2018: Creating UCSC Compatible files; make sure tabix and bgzip are available in the environment or this will not work.
Do 11. Okt 18:24:48 CEST 2018: Loop_PETs=59
Thu Oct 11 18:24:48 CEST 2018: 
['/usr/bin/Rscript', u'HiChIPper_full/qcReport.R', '/usr/local/lib/python2.7/dist-packages/hichipper', 'HiChIPper_full', '/home/Desktop/Software/HiChipper', '0.7.3', 'HiChIP']
/home/Desktop/Software/HiChipperUsing count as value column: use value.var to override.
Processing: HiChIP
Error in { : task 1 failed - "need at least four unique 'x' values"
Calls: %do% -> <Anonymous>
Execution halted

this is the output folder:

-rw-rw-r-- 1 home   2389 Okt 11 18:25 HiChIPper_full.hichipper.log
-rw-rw-r-- 1 home 377774 Okt 11 18:24 HiChIPper_full.hichipper.qcreport.html
-rw-rw-r-- 1 home 230555 Okt 11 18:24 HiChIP.anchors.bed
-rw-rw-r-- 1 home   2498 Okt 11 18:24 HiChIP.filt.intra.loop_counts.bedpe
-rw-rw-r-- 1 home   1780 Okt 11 18:24 HiChIP.interaction.txt.gz
-rw-rw-r-- 1 home   3513 Okt 11 18:24 HiChIP.interaction.txt.gz.tbi
-rw-rw-r-- 1 home    721 Okt 11 18:24 HiChIP.inter.loop_counts.bedpe
-rw-rw-r-- 1 home  24543 Okt 11 18:24 HiChIP.intra.loop_counts.bedpe
-rw-rw-r-- 1 home    499 Okt 11 18:24 HiChIP.stat

Thank you for your time,

Raphael

[caleblareau]

Here, the error is in the 59 Mapped_unique_intra_quality_anchor_med reads. Basically, you have such little PET density in your anchors, that the models being fit can't proceed as one would need to complete the downstream parts.

[vidaletal]

Many thanks, Closing the thread!