d-cameron
commented
7 years ago If I use the run instructions in the README instead of cmd I get:
$ Weaver PLOIDY -f SIMU.fa -S FINAL_SV -s SNP -g REGION -w X.bam.wig -r 0 -m map100mer.bd -p 64
RUN MODE PLOIDY
THREAD was set to 64.
FASTA was set to SIMU.fa.
WIG was set to X.bam.wig.
MAP was set to map100mer.bd.
SV was set to FINAL_SV.
SNP was set to SNP.
GAP was set to REGION.
RUNFLAG was set to 0.
Getting coverage profile...
Getting coverage profile done!
Getting GC content done!
Getting Mapability done!
Estimated cancer haplotype coverage: 0
Estimated normal haplotype coverage: 0
$ ll
total 1071780
-rw-r----- 1 cameron.d allstaff 405 Oct 30 2014 cmd
drwxr-x--- 2 cameron.d allstaff 9 May 29 11:59 INPUT
drwxr-x--- 2 cameron.d allstaff 10 Nov 4 2014 OUTPUT
-rw-r--r-- 1 cameron.d allstaff 0 May 29 12:01 TARGET
-rw-r--r-- 1 cameron.d allstaff 0 May 29 12:01 tempfile
-rw-r----- 1 cameron.d allstaff 1097298665 Oct 30 2014 X.bam
-rw-r----- 1 cameron.d allstaff 161816 Oct 30 2014 X.bam.bai
I have installed weaver from github to ~/weaver and unpacked Weaver_data.tar.gz and Weaver_example.tar.gz to the Weaver_data and Weaver_example sub-directories respectively. I have fixed the broken symlinks in ~/weaver/data
I am attempting to run the example. When I rerun Weaver_example/cmd I get the following output:
Note that the files are almost all empty files and are located in the ~/weaver/Weaver_example directory, not the ~/weaver/Weaver_example/OUTPUT subdirectory.
What else is required to reproduce the example output for the supplied example? Are you able to supply a working shell script that performs all weaver steps from just a just a (small) bam file, a reference fa, and the minimal set of additional files?
The example INPUT directory contains many input files for which there does not appear to be any instructions on how to generate these files. I am attempting to run weaver against a hg38 bam file and it is very unclear what files I need from where (e.g. the example includes a map100mer.bd file, but the ENCODE mappability tracks are in bigWig format and there does not appear to be any conversion instructions; it looks like a 4 column .bed file but there's no header and I don't know of column 4 is rescaled).