Error at Step1: Bowtie alignment

[HNK]

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

and have attached the config-hicpro file.

[HNK]

Can anyone help me please.

[nservant]

Hi,

Could you have a look to the bowtie logs in the `log` folder please ?

Best

[HNK]

##HiC-Pro mapping
/mnt/appl/HiC-Pro_2.11.4/scripts/hic.inc.sh: line 86: /mnt/appl/depedencies/bowtie2-2.4.1-linux-x86_64/bowtie2: No such file or directory

te bowtie2 is in this path.

[nservant]

So it seems that the bowtie2 path which is in the config-system.txt file (in the installation folder) is not correct ?

You can update the config-system.txt file directly ...

[HNK]

$ which bowtie2

/usr/local/bin/bowtie2

$ which samtools

/usr/local/bin/samtools

$ which python

/usr/bin/python

$ which R
/usr/bin/R

[nservant]

please remove the name of executable from the path ...

BOWTIE2_PATH = /usr/local/bin/
...

[HNK]

athsnks

its woring now.

Just a quick question, what is the pipeline terminates at step 2 or 3, can we rerun from that point again or really have to rerun from the start (as it really takes long for mapping)

[nservant]

Yes, have a look at '-s' options.

Note that you can specify serveral '-s' option.

In this case, the data should be organized as usual with one folder per sample.

Best