Problem when running make file

[metageni]

Hi there, Thanks for creating cleancall.

I describe below some problems that I'm having with the tool:

I ran cctools pileupas described in the documentation: -loci VCF file and --index tabular_file_with_sampleID_bam_path.

I get the following error message:

Finished generating CAPT Makefile Running 10 parallel jobs of CAPT make -f t.pileup.Makefile -j 10 /bin/sh: 1: set: Illegal option -o pipefail make: *** [t.pileup.sample1.txt.gz.tbi] Error 2

I opened the makefile (*.pileup.Makefile) and I was able to copy and run the lines manually. With exception of (echo "#FAM_ID IND_ID FAT_ID MOT_ID SEX MPU"; cut -f 1 bam.man | perl -lane 'print join("\t",$$F[0],$$F[0],0,0,0,"output2.pileup.".$$F[0].".txt.gz")') > output2.pileup.ped

That i believe it is necessary to edit it (?!) to where it was $$F[0] -> $F[0]

Here is the command I ran: cctools pileup --loci VCF --index tabular_file_with_sampleID_bam_path --out output2.pileup --ref REF_genome --run 10

So there are two possible problems: 1) Makefile is not running correctly after the cctools pileup call and (maybe missing to install something (?!)) and 2) maybe the way that pileup.ped is generated may be problematic.

Thank you!!!

[fredsamhaak]

Hi @hyunminkang,

I also encounter the same problem as @metageni and have no idea how to deal with it.

Thank you very much!