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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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the error everyone got but with different causes #315

Closed AhlemBoudell closed 3 years ago

AhlemBoudell commented 4 years ago

Hello HiC-pro folks,

so when I run the command:

HiC-Pro -i AllSamples -o AllResults -c config-hicpro.txt

i get the error:

/sw/csi/hicpro/2.10.0/el7_gnu6.4.0/HiC-Pro_2.10.0/scripts/bowtie_wrap.sh -c /ibex/scratch/projects/c2053/config-hicpro.txt -u >> hicpro.log Exit: Error in Bowtie alignment make: *** [bowtie_global] Error 1

here is the config file: config-hicpro.txt

Hicpro log file: hicpro.log

and one of the 2 log files of the 2 replicas: bowtie_H3K9_me_dimut_H5LGHCCX2_L5_R1_global_ce11.log

Any idea how to solve this?

nservant commented 4 years ago

Hi, Actually, the config file you are using is not the one from the HiC-pro 2.10 version. The FORMAT parameter is missing in the config.

I would suggest to update HiC-Pro to the latest version 2.11.XX, which should match your config and which does not need any quality format. best

AhlemBoudell commented 4 years ago

Thanks alot for the fast response!

I am using this version in our cluster and thats the only version we have apparently. Is there a way I can just modify my config file to make it work?

nservant commented 4 years ago

Just download the 2.10 version, and use the config file within this version. In theory, you should have a FORMAT option which is passed to bowtie2, using --${FORMAT}-quals With the previous bowtie2 version, it supported --phred33-quals options ... the point is that according to the manual, it doesn't see it is still the case with recent version. So have a look at your bowtie version first

AhlemBoudell commented 4 years ago

bowtie2 version: bowtie2/2.3.3.1

AhlemBoudell commented 4 years ago

It worked!

the command is running in the cluster for almost 18 hrs but with no errors at least.

Thanks alot .. was not going to figure it out by my self!

AhlemBoudell commented 4 years ago

Wed Feb 26 17:41:43 +03 2020 Bowtie2 alignment step1 ... /sw/csi/hicpro/2.10.0/el7_gnu6.4.0/HiC-Pro_2.10.0/scripts/bowtie_wrap.sh -c /ibex/scratch/projects/c2053/config-hicpro.txt -u >> hicpro.log

It has been on the first step since yesterday, and I just noticed that in other examples it didnt take nearly as much time as that! Is this ok?

nservant commented 4 years ago

Well, I would say it depends how many reads you have in input. did you split the reads per chunck to speed up the process ?