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tomazc / iCount

iCount, protein-RNA interaction analytics
http://icount.biolab.si
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peaks: [OSError] 28 #124

Closed nebo56 closed 7 years ago

nebo56 commented 7 years ago

I'm not sure why I get the following error for this data set:

Executing the following command: iCount peaks --half_window 10 --fdr 0.05 --perms 100 genes.gtf.gz iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed.10nt.peaks.bed --scores iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed.10nt.scores.tsv
Input parameters for function 'run' in iCount.analysis.peaks
    annotation: genes.gtf.gz
    sites: iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed
    peaks: iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed.10nt.peaks.bed
    scores: iCLIP_PTB_HeLa_WT_Hs.iCLIP2.Ule-xlink-sum.bed.10nt.scores.tsv
    features: None
    group_by: gene_id
    merge_features: False
    half_window: 10
    fdr: 0.05
    perms: 100
    rnd_seed: 42
    report_progress: False
Loading annotation file...
48075 out of 48075 annotation records will be used (0 skipped).
Loading cross-links file...
Calculating intersection between annotation and cross-link file...
[OSError] 28
  File "/home/skgthab/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/cli.py", line 438, in main
    result_object = func(**args)

  File "/home/skgthab/programs/ENV/lib/python3.5/site-packages/iCount-2.0.0.dev0-py3.5.egg/iCount/analysis/peaks.py", line 463, in run
    overlaps = annotation.intersect(sites, sorted=True, s=True, wo=True).saveas()

  File "/home/skgthab/programs/ENV/lib/python3.5/site-packages/pybedtools-0.7.8-py3.5-linux-x86_64.egg/pybedtools/bedtool.py", line 775, in decorated
    result = method(self, *args, **kwargs)

  File "/home/skgthab/programs/ENV/lib/python3.5/site-packages/pybedtools-0.7.8-py3.5-linux-x86_64.egg/pybedtools/bedtool.py", line 2908, in saveas
    compressed=compressed)

  File "/home/skgthab/programs/ENV/lib/python3.5/site-packages/pybedtools-0.7.8-py3.5-linux-x86_64.egg/pybedtools/bedtool.py", line 1211, in _collapse
    out_.writelines(in_)
JureZmrzlikar commented 7 years ago

ErrorCode 28 stands for "No space left on device". Please check if this is the case.

tomazc commented 7 years ago

This was already raised in an e-mail. You have to make sure that iCount.TMP_ROOT (or the bash variable ICOUNT_TMP_ROOT) points to a folder with enough free storage.