error n run tutorial

[bioinfo-dirty-jobs]

This is the comand that I use:

 nextflow run cipher.nf -with-singularity cipher.img --mode  chip --config  example_data/config.txt --fa /mnt/working_directory/Homo_sapiens.GRCh38.rel79.cdna.all.fa --gtf  /mnt/working_directory/Homo_sapiens.GRCh38.79.gtf --lib s --readLen 75
N E X T F L O W  ~  version 0.25.7
Launching `cipher.nf` [golden_becquerel] - revision: 553a48b852

                 RUN INFORMATION               
===============================================

mode:               chip
config:             /opt/cipher-workflow-platform-master/example_data/config.txt
fasta:              /mnt/working_directory/Homo_sapiens.GRCh38.rel79.cdna.all.fa
gtf:                /mnt/working_directory/Homo_sapiens.GRCh38.79.gtf
library:            s
read-length:            75

subsampled:         false

clumpify:           true
bbduk:              true
fastqc:             true
multiqc:            true
mapping:            true
bamcoverage:            true
downstream_analysis     true

threads:            1

aligner:            bbmap
===============================================

[warm up] executor > local
WARN: Access to undefined parameter `macs_g` -- Initialise it to a default value eg. `params.macs_g = some_value`
WARN: Access to undefined parameter `epic_egs` -- Initialise it to a default value eg. `params.epic_egs = some_value`
[22/abd8fe] Submitted process > calculate_egs
[80/e14b8c] Submitted process > clumpify (2)
[5f/7b7bcb] Submitted process > fetch_chrom_sizes
[25/e28a56] Submitted process > create_mapping_index
[f6/e92ae8] Submitted process > clumpify (1)
ERROR ~ Error executing process > 'clumpify (2)'

Caused by:
  Process `clumpify (2)` terminated with an error exit status (1)

Command executed:

  clumpify.sh -Xmx12g in=Input.500k_reads.fastq.gz out=Input_Rep1.clumped.fq.gz
  echo 'clumpify.sh -Xmx12g in=Input.500k_reads.fastq.gz out=Input_Rep1.clumped.fq.gz' > clumpify_parameters_Input_Rep1.txt

Command exit status:
  1

Command output:
  #
  # There is insufficient memory for the Java Runtime Environment to continue.
  # Native memory allocation (mmap) failed to map 4294967296 bytes for committing reserved memory.
  # An error report file with more information is saved as:
  # hs_err_pid24105.log

Command error:
  openjdk version "1.8.0_121"
  OpenJDK Runtime Environment (Zulu 8.20.0.5-linux64) (build 1.8.0_121-b15)
  OpenJDK 64-Bit Server VM (Zulu 8.20.0.5-linux64) (build 25.121-b15, mixed mode)
  java -ea -Xmx12g -Xms12g -cp /opt/anaconda2/opt/bbmap-37.17/current/ clump.Clumpify -Xmx12g in=Input.500k_reads.fastq.gz out=Input_Rep1.clumped.fq.gz
  OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00000006c0000000, 4294967296, 0) failed; error='Cannot allocate memory' (errno=12)

Work dir:
  /opt/cipher-workflow-platform-master/work/80/e14b8c1c8954af880c6eed4b5e2bd1

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Any suggestion ?Thanks so much!!!

[c-guzman]

You don't have enough memory to run the clumpify process. How much RAM does your machine have?

[bioinfo-dirty-jobs]

this machine have 4 G RAM...it is not my server it is laptop..

[c-guzman]

As you can see in the error report, clumpify uses 12GB of RAM to run. A lot of the processes require more than 4GB of RAM to run unfortunately, this is not something I can control with CIPHER but is built into the different tools that it uses.

Your best bet is to try this on a server or get a more powerful machine.

Try this command, and if it doesn't work then you'll need a more powerful computer.

nextflow run -qs 1 cipher.nf -with-singularity cipher.img --mode  chip --config  example_data/config.txt --fa /mnt/working_directory/Homo_sapiens.GRCh38.rel79.cdna.all.fa --gtf  /mnt/working_directory/Homo_sapiens.GRCh38.79.gtf --lib s --readLen 75 --downstream_analysis false --bamcoverage false --clumpify false --bbduk false 

This will stop most of the memory intensive downstream analysis and preprocessing (basically only mapping) as well as run only one process at a time. It won't do everything you want, but it will at least show that you were able to run CIPHER successfully.

[c-guzman]

Actually if that command doesn't work you can try this command and it SHOULD work. It basically only runs FastQC, but it'll be able to show you that CIPHER runs.

nextflow run -qs 1 cipher.nf -with-singularity cipher.img --mode  chip --config  example_data/config.txt --fa /mnt/working_directory/Homo_sapiens.GRCh38.rel79.cdna.all.fa --gtf  /mnt/working_directory/Homo_sapiens.GRCh38.79.gtf --lib s --readLen 75 --downstream_analysis false --bamcoverage false --clumpify false --bbduk false --mapping false

[bioinfo-dirty-jobs]

thanks that work!! So I can try to use on a server!!! Thanks so much!!!