Nothing to align ! Please check input files and R1/R2 extension

[mdozmorov]

Hi @nservant,

I have HiC-Pro running two jobs. The third job, config_hicpro_combined.txt set up identically, persistently results in the error

Bowtie2 alignment step1 ...
Nothing to align ! Please check input files and R1/R2 extension.
make: *** [/home/mdozmorov/.local/HiC-Pro_3.0.0/scripts/Makefile:88: bowtie_global] Error 1

I understand the folder structure, looked into the previous issue #195, but totally stuck. I use the identical folder structure for each job, same folder and subfolder names, configuration files. Only the content of *.fastq.gz files differ. Yet, two jobs run, and one is constantly failing. Any ideas?

Some diagnostic info:

rawdata/
└── Sample
    ├── Sample_R1.fastq.gz
    └── Sample_R2.fastq.gz

The PBS job is run from the output folder that has:

output/
├── config_hicpro_combined.txt
├── HiCPro_step1_PDX.sh
├── HiCPro_step2_PDX.sh
├── inputfiles_PDX.txt
├── logs
├── rawdata -> link/to/data
└── tmp

The cd $PBS_O_WORKDIR command is set. Attaching the config file. config_hicpro_combined.txt What could be wrong?

Thanks, Mikhail

[mdozmorov]

I was able to resolve it, so closing. The issue is that file- and folder's permissions should be owned but $USER who runs the jobs. Moreover, ALL folders and subfolders. It was very hard to pinpoint, because our file's permissions were set as -rwxrwxr-x, so all should have read access. Yet, it is the ownership that matter. I'd consider this a serious limitation that can easily take a week of postdoc's time to resolve. Hope it'll be fixed in the release branch.