How to fix 'File name too long' errors when using Snakemake
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When using Snakemake, I store the values for my variables as part of the filenames (ex. "processed/count_{project}.tsv"). Recently, I've started using R formulas with many covariates as a variable. Now I get an error because the the filename is too long for the operating system. Has anyone else run into this issue and have any suggestions? Is there a canonical Snakemake approach for this problem?
snakemake
asked Jan 4 at 16:06
wir963wir963
8618
add a comment |
When using Snakemake, I store the values for my variables as part of the filenames (ex. "processed/count_{project}.tsv"). Recently, I've started using R formulas with many covariates as a variable. Now I get an error because the the filename is too long for the operating system. Has anyone else run into this issue and have any suggestions? Is there a canonical Snakemake approach for this problem?
snakemake
asked Jan 4 at 16:06
wir963wir963
8618
Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14
add a comment |
When using Snakemake, I store the values for my variables as part of the filenames (ex. "processed/count_{project}.tsv"). Recently, I've started using R formulas with many covariates as a variable. Now I get an error because the the filename is too long for the operating system. Has anyone else run into this issue and have any suggestions? Is there a canonical Snakemake approach for this problem?
snakemake
asked Jan 4 at 16:06
wir963wir963
8618
When using Snakemake, I store the values for my variables as part of the filenames (ex. "processed/count_{project}.tsv"). Recently, I've started using R formulas with many covariates as a variable. Now I get an error because the the filename is too long for the operating system. Has anyone else run into this issue and have any suggestions? Is there a canonical Snakemake approach for this problem?
snakemake
snakemake
asked Jan 4 at 16:06
wir963wir963
8618
asked Jan 4 at 16:06
wir963wir963
8618
asked Jan 4 at 16:06
wir963wir963
8618
asked Jan 4 at 16:06
wir963wir963
8618
asked Jan 4 at 16:06
wir963wir963
8618
8618
Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14
add a comment |
Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14
Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14
add a comment |
1 Answer
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Personally, I don't think it is a good idea to store information into the filename.
Rather, I would create a temp file in tabular or yaml format linking the file in question to covariates or other data. Then read this file in R or else to extract the relevant information.
answered Jan 8 at 14:35
darioberdariober
1,1401223
add a comment |
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Personally, I don't think it is a good idea to store information into the filename.
Rather, I would create a temp file in tabular or yaml format linking the file in question to covariates or other data. Then read this file in R or else to extract the relevant information.
answered Jan 8 at 14:35
darioberdariober
1,1401223
add a comment |
Personally, I don't think it is a good idea to store information into the filename.
Rather, I would create a temp file in tabular or yaml format linking the file in question to covariates or other data. Then read this file in R or else to extract the relevant information.
answered Jan 8 at 14:35
darioberdariober
1,1401223
add a comment |
Personally, I don't think it is a good idea to store information into the filename.
Rather, I would create a temp file in tabular or yaml format linking the file in question to covariates or other data. Then read this file in R or else to extract the relevant information.
answered Jan 8 at 14:35
darioberdariober
1,1401223
Personally, I don't think it is a good idea to store information into the filename.
Rather, I would create a temp file in tabular or yaml format linking the file in question to covariates or other data. Then read this file in R or else to extract the relevant information.
answered Jan 8 at 14:35
darioberdariober
1,1401223
answered Jan 8 at 14:35
darioberdariober
1,1401223
answered Jan 8 at 14:35
darioberdariober
1,1401223
answered Jan 8 at 14:35
darioberdariober
1,1401223
1,1401223
add a comment |
add a comment |
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Which OS? I have run into this in Windows in the past (unrelated to snakemake). I would think it is an OS issue rather than having to do with snakemake. You may want to find ways to shorten filenames.
– JeeYem
Jan 4 at 18:28
@JeeYem I get the error on both Mac (Mojave) and Linux OS. In short, my question is whether there is a canonical Snakemake way to shorten filenames. Obviously, I could hack something together to shorten the filenames but I want to see if anyone has a better approach
– wir963
Jan 4 at 19:14