HiC-PRo step 1 error

Question

[HK]

Hi

I am trying to run HiC-Pro for the verty first time but get this error.

Run HiC-Pro 2.11.4
--------------------------------------------
Mon Sep  7 16:49:52 CEST 2020
Bowtie2 alignment step1 ...
Logs: logs/p841sHU_xx_chip_pe_Papantonis_B_1/mapping_step1.log
[main_samview] fail to read the header from "-".
[main_samview] fail to read the header from "-".
Exit: Error in reads alignment - Exit
make: *** [/mnt/appl/dependencies/HiC-Pro-2.11.4/bin/../scripts//Makefile:88: bowtie_global] Error 1

Command used is :

./HiC-Pro -i /mnt/data/Taneja/ -o /mnt/data/output_HiC -c /mnt/appl/HiC-Pro_2.11.4/config-hicpro.txt

Answer 1

[jamzaleg84]

Hi, I don't know if you've received an answer yet, but I had the same issue when trying to run it yesterday and I posed the question to the developer of the program and he suggested it could be an issue with how the fastq files are presented in your directory vs how they are alluded to in the config-hicpro.txt file.

Here's my exchange with him if it helps:

https://github.com/nservant/HiC-Pro/issues/400