[merge_valid_interactions] Erreur 1

[PFRoux]

Hi !

First of all, thanks a lot for this really nice tool.

I am trying to setup a fresh install of HiC-Pro 3.0.0 on our cluster, but - after successfully running the workflow on the test data set, I am having the following issue with my HiChIP data :

lun. mars 29 17:30:29 CEST 2021
Merge chunks from the same sample ...
Logs: logs/shp53mDox_HiChIP_H3K27ac_r1_CHR22/merge_valid_interactions.log
make: *** [merge_valid_interactions] Erreur 1

Here is what I get in the log file :

pfroux@genologin1 ~/work/P53_HICHIP/Test/Data $ more 4-HIC-PRO/OUTPUT/logs/shp53mDox_HiChIP_H3K27ac_r1_CHR22/merge_valid_interactions.log
## Merge valid interactions for shp53mDox_HiChIP_H3K27ac_r1_CHR22 - fastq - hic_results/data/...
## Remove duplicates ...
LANG=en; sort -T tmp -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m hic_results/data//shp53mDox_HiChIP_H3K27ac_r1_CHR22/shp53mDox_HiChIP_H3K27ac_r1
_CHR22_hg19.bwt2pairs.validPairs | awk -F"\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=$2 || c2!=$5 || s1!=$3 || s2!=$6){print;c1=$2;c2=$5;s1=$3;s2
=$6}' > hic_results/data//shp53mDox_HiChIP_H3K27ac_r1_CHR22/shp53mDox_HiChIP_H3K27ac_r1_CHR22.allValidPairs
shp53mDox_HiChIP_H3K27ac_r1_CHR22	106652
## Select valid interactions from capture target ...
/tools/python/3.7.4/bin/python /usr/local/bioinfo/src/HiC-Pro//HiC-Pro_3.0.0/scripts/onTarget.py -i hic_results/data//shp53mDox_HiChIP_H3K
27ac_r1_CHR22/shp53mDox_HiChIP_H3K27ac_r1_CHR22.allValidPairs -t /work/pfroux/P53_HICHIP/Test/Data/3-PEAK-CALLING/shp53mDox_HiChIP_H3K27ac
_r1_CHR22_MACS2_peaks.narrowPeak -s hic_results/stats//shp53mDox_HiChIP_H3K27ac_r1_CHR22/shp53mDox_HiChIP_H3K27ac_r1_CHR22_allValidPairs.m
ergestat -v > hic_results/data//shp53mDox_HiChIP_H3K27ac_r1_CHR22/shp53mDox_HiChIP_H3K27ac_r1_CHR22_ontarget.allValidPairs
  File "/usr/local/bioinfo/src/HiC-Pro//HiC-Pro_3.0.0/scripts/onTarget.py", line 132
    print("## Opening valid pairs file {}...".format(inFile), file=sys.stderr))
                                                                              ^
SyntaxError: invalid syntax

It looks like a python-related error. But what I don't understand is why is it working with the test dataset and not mine ? Do you have any idea ?

Thanks a lot for your help.

++

Pef

[PFRoux]

I think it's related to the fact I am using a CAPTURE_TARGET argument.

[sfpacman]

The onTarget.py is buggy . The print function has an extra bracket ( - you need to take it out.

There is another bug on line 58 with open(infile, 'r') as bed_handle: . It should be in_file if you look at line 44.

After I manually made those changes on my local copy, I didn't encounter any further error

[nservant]

Hi, Yes the devel is corrected. You can use it if you wish I'll make a new release soon N