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WeichenZhou / PALMER

Pre-mAsking Long reads for Mobile Element inseRtion
MIT License
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BLAST too many postional arguments #15

Closed chadsmith123 closed 4 years ago

chadsmith123 commented 4 years ago

Describe the bug Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /fastscratch/smithch/beck-lab/Mice/PacBio/palmer/PWD_CHRX2/PALMER//chrX_1_1000000/SEQ.masked

To Reproduce

Desktop (please complete the following information):

Additional context Using --custom-seq flag and BLAST 2.9.0+

stderr.txt stdout.txt

WeichenZhou commented 4 years ago

Hi Chad!

Sorry for the delay.

Did you get any sub-folders in your working directory? If yes, does it have any files? If no, would you try the working directory as '''--workdir /fastscratch/smithch/beck-lab/Mice/PacBio/palmer/PWD_CHRX2/PALMER/''' not '''--workdir /fastscratch/smithch/beck-lab/Mice/PacBio/palmer/PWD_CHRX2/PALMER//'''

Thanks! Arthur

WeichenZhou commented 4 years ago

In addition, it seems missing a parameter '--type' as input. As I can see here, it would be '--type CUSTOMIZED'. And you want to open TSD finder option as well: '--TSD_finding TRUE', since you still want to find out the retrotransposition events.

Here is an example when I ran PALMER for NumtS in Chimpanzee: '''./PALMER --input $DirPath/your.bam.file --workdir $DirPath/ --ref_ver other --output your.output.prefix --chr chr5 --ref_fa $your.reference.file.path/your.reference.fa --type CUSTOMIZED --custom_seq $your.custom_seq.file.path/Clint.mt'''

WeichenZhou commented 4 years ago

I added one more example in the readme file, please try the example here:

./PALMER --input $DirPath/your.bam.file --workdir $DirPath/ --output your.output.prefix --chr chrX --ref_ver other --ref_fa $your.reference.file.path/your.reference.fa --type CUSTOMIZED --custom_seq $your.custom_seq.file.path/L1MdA_consensus.fa --custom_index $your.custom_index.file.path/mm10_ucsc_repeatmasker_LINE.bed --TSD_finding TRUE

Also, if it still not working, that would be good if you could provide us a ref fasta and a sample BAM so we can trouble shoot locally.

Thanks!

WeichenZhou commented 4 years ago

Will close it if no more discussion in this issue.

WeichenZhou commented 4 years ago

Close the issue.