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institut-de-genomique / NaS

NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions.
http://www.genoscope.cns.fr/nas/
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/home/NGSResources/bin/NaS_wrapped: line 199: /usr/bin/cat: Argument list too long #6

Closed mebbert closed 8 years ago

mebbert commented 8 years ago

I just ran into the following error:

/home/NGSResources/bin/NaS_wrapped: line 199: /usr/bin/cat: Argument list too long

The ./tmp/psl directory has 47,661 files in it.

I changed line 199 from

cat $OUTPUT_DIR/tmp/psl/*.psl | awk -v PFX=$OUTPUT_DIR/reads '{ file=PFX"/"$14".psl"; print $0>file; }'

to

for i in $OUTPUT_DIR/tmp/psl/*.psl do cat $i | awk -v PFX=$OUTPUT_DIR/reads '{ file=PFX"/"$14".psl"; print $0>file; }' done

Let me know if I misunderstood and messed up the purpose of this step.

I appreciate your help!

ghost commented 8 years ago

Hi,

the number of files produced depends on the amount of nanopore reads you have. Your command seem to do the exact same job as our (but for large amount of files). I think you can run it without problem (i'll discuss this issue with the NaS team for further implementation).

However i think that's not the only "cat" of NaS (so you will certainly encounter other "cat" problems).

If you encounter other issues do not hesitate to ask.