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fastqc; VM maximum heap size error

Nov 5th, 2021
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  1. Configuring section "assemble" from "/mnt/scgc_nfs/opt/conf/nextseq.yaml"
  2. Configuring section "shared" from "/mnt/scgc_nfs/opt/conf/nextseq.yaml"
  3. Configuring section "join" from "/mnt/scgc_nfs/opt/conf/nextseq.yaml"
  4. Configuring section "deliverables" from "/mnt/scgc_nfs/opt/conf/nextseq.yaml"
  5. Configuring section "coassemble" from "/mnt/scgc_nfs/opt/conf/nextseq.yaml"
  6. [2021-11-05 10:25:03,775 Assemble INFO] Assembly started on AH-806-J10
  7. [2021-11-05 10:25:03,802 Assemble INFO] Writing results to /mnt/scgc_raw/results/nextseq/210408_VH00511_2_AAAFFWNHV/AH-806-J10
  8. [2021-11-05 10:25:09,608 scgc.utils INFO] Running FastQC
  9. [2021-11-05 10:25:09,608 scgc.utils INFO] $> fastqc --outdir /mnt/scgc_raw/results/nextseq/210408_VH00511_2_AAAFFWNHV/AH-806-J10/AH-806-J10_WGS_QC/AH-806-J10_fastqc/tmpRsVQBb --noextract -f fastq -t 12 -q /mnt/scgc_raw/data/nextseq/210408_VH00511_2_AAAFFWNHV/Data/Intensities/BaseCalls/AH-806-J10_R1.fastq.gz
  10. Error occurred during initialization of VM
  11. Could not reserve enough space for 3072000KB object heap
  12. Traceback (most recent call last):
  13. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/bin/scgc", line 11, in <module>
  14. load_entry_point('scgc', 'console_scripts', 'scgc')()
  15. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click/core.py", line 722, in __call__
  16. return self.main(*args, **kwargs)
  17. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click/core.py", line 697, in main
  18. rv = self.invoke(ctx)
  19. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
  20. return _process_result(sub_ctx.command.invoke(sub_ctx))
  21. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click/core.py", line 895, in invoke
  22. return ctx.invoke(self.callback, **ctx.params)
  23. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click/core.py", line 535, in invoke
  24. return callback(*args, **kwargs)
  25. File "/mnt/scgc_nfs/opt/common/anaconda/2.1.0/lib/python2.7/site-packages/click_config/__init__.py", line 45, in wrapper
  26. return fn(**kwargs_to_forward)
  27. File "/mnt/scgc/scgc_nfs/opt/scgcpy/scgc/__main__.py", line 503, in scgc_assemble
  28. [r1, r2], op.join(qc_dir, sample + "_fastqc"), config.assemble.cores
  29. File "/mnt/scgc/scgc_nfs/opt/scgcpy/scgc/apps.py", line 110, in run_fastqc
  30. description="Running FastQC")
  31. File "/mnt/scgc/scgc_nfs/opt/scgcpy/scgc/utils.py", line 195, in run
  32. raise subprocess.CalledProcessError(p.returncode, cmd=cmd)
  33. subprocess.CalledProcessError: Command 'fastqc --outdir /mnt/scgc_raw/results/nextseq/210408_VH00511_2_AAAFFWNHV/AH-806-J10/AH-806-J10_WGS_QC/AH-806-J10_fastqc/tmpRsVQBb --noextract -f fastq -t 12 -q /mnt/scgc_raw/data/nextseq/210408_VH00511_2_AAAFFWNHV/Data/Intensities/BaseCalls/AH-806-J10_R1.fastq.gz' returned non-zero exit status 1
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