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mshabbirhasan / ups-indel

UPS-indel is a tool for "Universal Positioning System" of indels. It can be used to compare indels to see whether they are biologically equivalent or not. It can also be used to find out redundant indels. Moreover UPS-indel can be used to compare indels called by different tools.
MIT License
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rm: cannot remove ‘example/real_test.*.uvcf’: No such file or directory #1

Open MaxSalm opened 6 years ago

MaxSalm commented 6 years ago

Hi there,

Thank you for your program! I've succesfully compiled the code and tested it on the provided examples . However, when testing it on independent data (using hg19.fa and a VCFv4.1 output from Scalpel) I encounter the following error:

rm: cannot remove ‘example/real_test.*.uvcf’: No such file or directory

All help would be welcome!

P.s. I've also noticed that if the code is not executed from the package directory, then the following error is encountered:

Error: Unable to access jarfile ext/SnpSift.jar

mshabbirhasan commented 6 years ago

Thanks for using UPS-indel. While we are working on this error message, a quick workaround is to navigate to the UPS-indel directory and run the executables from that directory.

rohandavidg commented 6 years ago

Hi,

Thank you for this program, however I seem to be having the same issue even though i'm in the UPS-indel directory

./ups_indel \ /research/gatk_bundle/human/2.8/b37/processed/2015_11_04/allchr.fa \ /research/indel_concordance/gatk/s_NA24385-son.haplotypecaller.vcf \ /research/indel_concordance/gatk/out \ -hd=true

rm: cannot remove `/research/indel_concordance/gatk/out.*.uvcf'

Thank you for your assistance

Thanks, Rohan

mshabbirhasan commented 6 years ago

Hi Rohan,

Thanks for using UPS-indel. Regarding the problem you mentioned, could you please check if you have permission to remove a file from that directory? Looks like it is the permission issue.

I'll try to find an alternative way to remove the temporary UVCF files. Despite the problem with the removal of temporary files, your final output UVCF file should be produced with no problem, could you please check that?

Thanks, Mohammad

bcantarel commented 5 years ago

I have tried running UPS-Indel with my own data: 1) I had to update the cpp with the location of my local SnpSift.jar If this is not updated, I get the same error as the other issue: ./ups_indel example/ref.fa example/in.vcf example/out -hd=true Error: Unable to access jarfile SnpSift.jar rm: cannot remove ‘example/in..vcf’: No such file or directory rm: cannot remove ‘example/out..uvcf’: No such file or directory

I have added the full path to the code for the location of SnpSift.jar and this example data now works.

2) I also get this error with my own data files and the properly located SnpSift.jar [ups-indel]$ ./ups_indel /project/shared/bicf_workflow_ref/human/GRCh38/genome.fa ~/HD829.scapel.vcf ~/out -hd=true Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 rm: cannot remove ‘/archive/PHG/PHG_Clinical/devel/idt_heme_panel/pipeline_devel/analysis_vc/HD829/dna/HD829.scapel_uvcf.*.uvcf’: No such file or directory

If I copy my VCF file to example/in.vcf and my reference to example/ref.fa (and the faidxf file)-- I get the same error: [ups-indel]$ ./ups_indel example/ref.fa example/in.vcf example/out -hd=true Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 rm: cannot remove ‘example/out.*.uvcf’: No such file or directory

My sequences have chr ie chr1, etc -- does that matter?

bcantarel commented 5 years ago

BTW -- this error indicates that no output has been generated it is not a permissions issue.