"*_temporary_hichipperPeaks.bed_pad.bed.tmp" has size 0 issue

[shanwai1234]

Hello,
I run Hichipper to infer peaks from my data, however, it always gives me this error below, could you help me to figure it out? Thank you!

Sun Sep 06 12:52:34 CDT 2020: Starting hichipper pipeline v0.7.0
Sun Sep 06 12:52:34 CDT 2020: Parsing user parameters
/home/springer/liang795/anaconda3/envs/py27/lib/python2.7/site-packages/hichipper/cli.py:19: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
m = yaml.load(f)
Sun Sep 06 12:52:36 CDT 2020: Performing hichipper-modified background peak calling
Sun Sep 06 12:53:44 CDT 2020: Modified background signal; performing peak calling
Sun Sep 06 12:53:44 CDT 2020: MACS2 TEXT OUTPUT INCOMING
INFO @ Sun, 06 Sep 2020 12:53:45: Read and build treatment bedGraph...
INFO @ Sun, 06 Sep 2020 12:53:45: Read and build control bedGraph...
INFO @ Sun, 06 Sep 2020 12:53:45: Build scoreTrackII...
INFO @ Sun, 06 Sep 2020 12:53:45: Calculate scores comparing treatment and control by 'qpois'...
INFO @ Sun, 06 Sep 2020 12:53:45: Write bedGraph of scores...
INFO @ Sun, 06 Sep 2020 12:53:45: Finished 'qpois'! Please check 'hichipper-test/hichipper_qvalue.bdg.tmp'!
INFO @ Sun, 06 Sep 2020 12:53:46: Read and build bedGraph...
INFO @ Sun, 06 Sep 2020 12:53:46: Call peaks from bedGraph...
INFO @ Sun, 06 Sep 2020 12:53:46: Write peaks...
INFO @ Sun, 06 Sep 2020 12:53:46: Done
Warning message:
In fread(peaksfile, header = FALSE) :
File 'hichipper-test/test_temporary_hichipperPeaks.bed_pad.bed.tmp' has size 0. Returning a NULL data.table.
Error in .find_seqnames_col(df_colnames0, seqnames.field0, prefix) :
cannnot find seqnames column
Calls: makeGRangesFromDataFrame -> .find_GRanges_cols -> .find_seqnames_col
Execution halted
Sun Sep 6 12:54:09 CDT 2020: Processing test
Sun Sep 6 12:54:09 CDT 2020: Total_PETs=2500
Sun Sep 6 12:54:09 CDT 2020: Mapped_unique_quality_pairs=1101
Sun Sep 6 12:54:09 CDT 2020: Mapped_unique_quality_valid_pairs=302
Sun Sep 6 12:54:09 CDT 2020: Intersecting PETs with anchors
Error: The requested file (/scratch.global/liang795/HiChip/seedling_hichip_20190626/SmallTest/hichipper-test/test_temporary_hichipperPeaks.bed_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting!
Sun Sep 6 12:54:09 CDT 2020: Bedtools does not exist, but we need it
ERROR: something failed at the individual sample level; check the .log file for more info

[caleblareau]

Try these two things

1. hopefully this works-- can you make sure that bedtools is in your environment?

2. Another potential issue is that your samples may not be calling any peaks