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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Make error #493

Open Jaureguy760 opened 2 years ago

Jaureguy760 commented 2 years ago

Hi, I am currently running HiC-Pro with a few different datasets. I have run into an error with one run. I have included the files and scripts below attached. I have been attempting to debug for a week now and figured it was time to reach out for some assistance.

Best, Jeff Jaureguy

Error message:

make: mkdir: No such file or directory make: *** [/iblm/netapp/home/jjaureguy/bin/HiC-Pro/scripts/Makefile:75: configure] Error 127 config-hicpro_KG.txt

[config-hicpro_KG.txt](htt HiCPro_step1_KG_split.txt ps://github.com/nservant/HiC-Pro/files/7477595/c HiCpro_s1_KG_split.o7526187.1.txt inputfiles_KG_split.txt

nservant commented 2 years ago

Hi Jeff, So you were already able to run it on other datasets ? this is the only one which crashed ? It is not clear to me where it crashed ? does it start running something ?

Jaureguy760 commented 2 years ago

Hi,

No, the program does output any log files just the error below. What's stranger is the temp file is already generated. So I do not know why this error message is being flagged.

error: make: mkdir: No such file or directory make: *** [/iblm/netapp/home/jjaureguy/bin/HiC-Pro/scripts/Makefile:75: configure] Error 127

However, it looks like for all 3 runs. I'm running into this other issue for some of my samples. I have attached a previous user's issue with this to determine if this is the solution that he proposed. Do you have any suggestions on this issue? It seems like this message has propagated for the remaining samples that have not been processed properly.

Error:

Fri Nov 5 12:21:59 PDT 2021 Bowtie2 alignment step1 ... Nothing to align ! Please check input files and R1/R2 extension. make: *** [/iblm/netapp/home/jjaureguy/bin/HiC-Pro/scripts/Makefile:89: bowtie_global] Error 1

[https://github.com/nservant/HiC-Pro/issues/360]

Jaureguy760 commented 2 years ago

I think I found out with regards to my first issue it was server-related.

I'm still working on trying to understand the 2nd issue? It looks like people have had this issue in the past on the previous version. Please advise.

Best.

nservant commented 2 years ago

Hi, It seems that the input files are not detected. Could you please, show me the content of your input folder ? you should have one folder per sample and the fastq file extension should match what you have in the config file (PAIR1_EXT / PAIR2_EXT) Thanks