hichipper in CALL mode

[md1587]

Hi,
I'm testing hichipper in different modes, and I am having problems with the CALL mode.
I am running the latest version (0.7.7) and tested different possibilities:

1. CALL mode with a single valid interaction file as follows
   hichipper -o test_call --input-vi hicpro/hic_results/data/SRR3467175/SRR3467175.allValidPairs -p GM12878_SMC3.narrowPeak -rf MboI_resfrag_hg19.bed call
   This generates all the files (non empty) but failed the generation of the QC report. This is the message printed on screen:
   Mon Oct 07 16:04:19 CEST 2019: Starting hichipper pipeline v0.7.7
   Mon Oct 07 16:04:19 CEST 2019: Parsing user parameters
   Mon Oct 07 16:04:19 CEST 2019: Direct loop call option detected.
   Anchors removed due to excessive size (likely at ends of chromosomes): 18
   Mon Oct 7 16:05:04 CEST 2019: Processing one
   Mon Oct 7 16:05:04 CEST 2019: Intersecting PETs with anchors
   Mon Oct 7 16:05:04 CEST 2019: Finished the anchor merging.
   Mon Oct 7 16:05:04 CEST 2019: Finished the anchor processing.
   Mon Oct 7 16:31:09 CEST 2019: Intrachromosomal_valid_small=6549671
   Mon Oct 7 16:33:46 CEST 2019: Intrachromosomal_valid_med=29890131
   Mon Oct 7 16:35:34 CEST 2019: Intrachromosomal_valid_large=11695151
   Mon Oct 7 16:35:34 CEST 2019: Total number of anchors used: 53505
   Mon Oct 7 16:35:34 CEST 2019: Total number of reads in anchors: 10462287
   Mon Oct 7 16:48:17 CEST 2019: Mapped_unique_intra_quality_anchor=797794
   Mon Oct 7 16:48:17 CEST 2019: Mapped_unique_intra_quality_anchor_small=329852
   Mon Oct 7 16:48:17 CEST 2019: Mapped_unique_intra_quality_anchor_med=405133
   Mon Oct 7 16:48:17 CEST 2019: Mapped_unique_intra_quality_anchor_large=62818
   Mon Oct 7 16:48:19 CEST 2019: Loop_PETs=405133
   hicpro/hic_results/data/SRR3467175/SRR3467175.allValidPairs
   Mon Oct 07 16:48:19 CEST 2019:
   ['/usr/local/bin/Rscript', u'test_call/qcReport.R', '/usr/local/lib/python2.7/dist-packages/hichipper', 'test_call', '/home/martina/workspace/test_hichipper', '0.7.7', 'one']
   /home/martina/workspace/test_hichipperQuitting from lines 39-101 (qcReport_make.Rmd)
   Error in .fun(.value[0], ...) : invalid 'type' (character) of argument
   Calls: ... suppressMessages -> withCallingHandlers -> acast -> cast -> vaggregate
   Execution halted
   Processing: one

2. CALL mode with 2 valid interaction files:
   hichipper -o test_call_3 --input-vi hicpro/hic_results/data/SRR3467175/SRR3467175.allValidPairs,hicpro/hic_results/data/SRR3467176/SRR3467176.allValidPairs -p GM12878_SMC3.narrowPeak -rf MboI_resfrag_hg19.bed call
   But this is not starting at all. Here is the error message:
   Tue Oct 08 09:38:00 CEST 2019: Starting hichipper pipeline v0.7.7
   Tue Oct 08 09:38:00 CEST 2019: Parsing user parameters
   Tue Oct 08 09:38:00 CEST 2019: Direct loop call option detected.
   hicpro/hic_results/data/SRR3467175/SRR3467175.allValidPairs,hicpro/hic_results/data/SRR3467176/SRR3467176.allValidPairs
   ERROR: in call mode, specify --input-vi

From the --help of hichipper I understood that it was possible to pass a comma-separated list of valid interactions, but it seems that it is not recognising it as multiple inputs. I tried to repeat twice the --input-vi option with each file separately, but it recognised just the last one and then returned the same error as of point 1).
Besides, is there a way in CALL mode to keep the sample name instead of "one"?
The QC report, along with all the expected output files, is generated without any problem when supplying the manifest file as in the command below:
hichipper --out test1 config.yaml
where the config.yaml is:
peaks:

• GM12878_SMC3.narrowPeak
  resfrags:
• MboI_resfrag_hg19.bed
  hicpro_output:
• hicpro

Thank you very much for any help
Cheers
Martina

[wbszhu]

Hi，
I also have some problems
CALL mode with a single valid interaction file
########
Command
#######
hichipper --out ./hichipper_results --input-vi /data2/zhanglu/downsample.allValidPairs -p /data2/CTCF_peak.bed -rf /data2/22.genome/AluI.bed call
##########
Error
########
Thu Sep 24 10:52:13 CST 2020: Starting hichipper pipeline v0.7.7
Thu Sep 24 10:52:13 CST 2020: Parsing user parameters
Thu Sep 24 10:52:13 CST 2020: Direct loop call option detected.
Thu Sep 24 10:52:48 CST 2020: Processing one
Thu Sep 24 10:52:48 CST 2020: Intersecting PETs with anchors
Thu Sep 24 10:52:48 CST 2020: Finished the anchor merging.
Thu Sep 24 10:52:48 CST 2020: Something went wrong in determining peaks for anchor inference; rerun with the flag to debug.
/data2/zhanglu/downsample.allValidPairs
#########
Warning message:
In fread(peaksfile, header = FALSE) :
File './hichipper_results/userSuppliedPeaks.bed.tmp_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
Error: The requested file (./hichipper_results/userSuppliedPeaks.bed.tmp_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting!
/data2/zhanglu/miniconda2/envs/hichipper/lib/python2.7/site-packages/hichipper/interactionsCall_inputFrags.sh: line 35: --keep-temp-files: command not found
ERROR: something failed at the individual sample level; check the .log file for more info