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Long names not working #70

Closed morenomayar closed 10 years ago

morenomayar commented 11 years ago

I tried to run like this on eos (with the eos installation) and got a "name too long error":

bammds /home/jmoreno/data/my_kelvin_data/MDSTests/HGDPdata/HGDP_hg19.one_allele.txt /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00456.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00521.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00542.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00665.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00778.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00927.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP00998.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP01029.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP01284.flt.sort.rmdup.realign.md.bam /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/DownSampled_3e+05_HGDP01307.flt.sort.rmdup.realign.md.bam -o D3e+05.pdf

bammds: Error: Cannot write tmp/DownSampled_3e+05_HGDP00456.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00521.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00542.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00665.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00778.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00927.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP00998.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP01029.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP01284.flt.sort.rmdup.realign.md,DownSampled_3e+05_HGDP01307.flt.sort.rmdup.realign.md,HGDP_hg19.one_allele.legend.csv: File name too long

Is there a prefix-like way to solve this?

ole-tange commented 11 years ago

Idea:

Assume people are following the recommendation to name the bam files Population.Individual.something.bam.

If there are few bams name the tmp file:

pop1.indv1,pop2.indv2,pop3.indv3,reference.asd

If there are more:

pop1.indv1,pop2.indv2,pop3.indv3,reference+7,8BiUe.asd

where 8BiUe is a hash value of the 7 additional bams.

Since the names are only used internally I do not see a case where you would prefer to use your own prefix (except for the output and that can be set with -o).

ole-tange commented 11 years ago

This is now implemented in [287].

ole-tange commented 11 years ago

Test and close or report back.

morenomayar commented 11 years ago

Long names works great now!

morenomayar commented 10 years ago

Long names stopped working again =( I am running on eos and this one does not work:

time bammds /home/jmoreno/data/my_kelvin_data/MDSTests/HGDPdata/FlippedHGDP_hg19.one_allele.txt /home/jmoreno/data/my_kelvin_data/MDSTests/DownSampling/Down_3e+05_bam

I get:

bammds: Error: Cannot write tmp/DownSampled_3e+05_HGDP00456.flt,DownSampled_3e+05_HGDP00521.flt,DownSampled_3e+05_HGDP00542.flt,DownSampled_3e+05_HGDP00665.flt,DownSampled_3e+05_HGDP00778.flt,DownSampled_3e+05_HGDP00927.flt,DownSampled_3e+05_HGDP00998.flt,DownSampled_3e+05_HGDP01029.flt,DownSampled_3e+05_HGDP01284.flt,DownSampled_3e+05_HGDP01307.flt,FlippedHGDP_hg19.one_allele,.legend.csv: File name too long

ole-tange commented 10 years ago

Fixed in [303]. Please test and close if it works.

morenomayar commented 10 years ago

It works now! =D Thanks!