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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Error in postalign_xcor.bds', line 102 #135

Open beckedorff opened 5 years ago

beckedorff commented 5 years ago

Hi, I send a job with the command:

bds /nethome/fxf201/bin/encode_atac_update/atac_dnase_pipelines/atac.bds -species hg19 no_par -out_dir sh11_cy_ctrl -enable_idr -multimapping 4 -smooth_win 73 -auto_detect_adapter -nth 15 \ -fastq1_1 /scratch/projects/exempt/tr/felipe/ATAC_seq/new_atac_felipe/fastq_files/sh11_cy_ctrl_r1_R1.fastq-trimmed-pair1.fastq.gz \ -fastq1_2 /scratch/projects/exempt/tr/felipe/ATAC_seq/new_atac_felipe/fastq_files/sh11_cy_ctrl_r1_R1.fastq-trimmed-pair2.fastq.gz \ -fastq2_1 /scratch/projects/exempt/tr/felipe/ATAC_seq/new_atac_felipe/fastq_files/sh11_cy_ctrl_r2_R1.fastq-trimmed-pair1.fastq.gz \ -fastq2_2 /scratch/projects/exempt/tr/felipe/ATAC_seq/new_atac_felipe/fastq_files/sh11_cy_ctrl_r2_R1.fastq-trimmed-pair2.fastq.gz

and the pipeline worked until the xcor step. Here is the log file:

Thanks,

Felipe atac_ctrl_sh11.log

leepc12 commented 5 years ago

Please update your pipeline and reinstall dependencies. This is a known issue and has already been fixed.

$ git pull
$ bash uninstall_dependencies.sh
$ bash install_dependencies.sh

After re-installation, please check if you have run_spp.R on your $PATH

$ source activate bds_atac
$ which conda
$ which bedtools
$ which run_spp.R
Scubatuba99 commented 5 years ago

I am having a similar issue, and when I update the pipeline, I then get the problem listed in #110 and then when I update bds as mentioned as the fix I get this error again. So i'm stuck.

beckedorff commented 5 years ago

I had this issue after update my software, that's why the suggestion above did not solve my problem because appears just after the update and everything was in the correct localization.

I had re-install separated in the conda environment (bds_atac) numpy and r-spp ==1.13 that's how I fix the problem.

leepc12 commented 5 years ago

For those who are suffering from this issue, please reinstall dependencies. This error occurrs when one of the dependencies (run_spp.R) is not correctly installed.

$ bash uninstall_dependencies.sh
$ bash install_dependencies.sh

You should see a SUCCESS message at the end of the dep installation. Then it's okay to proceed.

visze commented 4 years ago

I have the same issue. I think in the conda files (requirements.txt) the phantompeakqualtools are missing. r-spp alone does not provide the script run_spp.R