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rgcgithub / clamms

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
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calc_window_mappability.py line 69 syntax error #13

Open AlexGreiner opened 6 years ago

AlexGreiner commented 6 years ago

Hi all,

I'm attempting to install/run CLAMMS on a high performance cluster at my University to call CNVs on exomes (aligned to hg19/GRCh37). I'm using CentOS Linux release 7.4.1708, x86_64 architecture, and I do not have root/sudo access. I'm seeking help on an issue I come across while running the annotate_windows.sh command.

My specific error output is: File "/Users/myname/clamms/calc_window_mappability.py", line 69 print "%s\t%d\t%d%s\t%.3f" % (window[0], window[1], window[2], window[3], ^ SyntaxError: invalid syntax

The command that generates this error is: $ ./annotate_windows.sh /Users/myname/Agilent*/Regions.bed /Users/myname/fasta/grch37/HomoSapiens.CLAMMS.fa /Users/myname/bed_files/mappability.bed $INSERT_SIZE /Users/myname/clamms/data/clamms_special_regions.hg19.bed >windows.bed

I performed all troubleshooting steps included in the installation instructions (https://github.com/rgcgithub/clamms), ensuring that my files were sorted and named properly (cut -f 1 *.bed | uniq). I noted that some bed files included mitochondrial, X, and Y chromosomes, as well as supercontigs --- this wasn't consistent between bed files, so I removed all supercontigs, as well as M, X, and Y chromosomes. M, X, and Y CNVs aren't of particular interest to me, as these inheritance patterns don't fit my model. I also checked the chromosome names in my FASTA file (grep '^>' -m 24 genome.fa). I also ensured the environment variables which needed to be set were set appropriately.

Can anybody provide some help on this error?

Thanks in advance.

squigzzz commented 1 year ago

I am having an identical issue, wondering if anybody can help out here.