Output argument "T" (and maybe others) not assigned during call to "readBams".

[sunfenghao2017]

this is my error: Output argument "T" (and maybe others) not assigned during call to "readBams". here is my params: bamList: /opt/workdir/mergency/bamlist ###path to file contining paths to bams regionsFile: /opt/workdir/DB/bed/xgen.idt.bed.anno.bed ###path to bed file defining regions targeted in exome snpVCFpath: /opt/workdir/DB/snpVCFs/ExAC.1000G.maxAF.merge.chr ###path to vcfs containg population frequencies (one for each chromosome), including part of filename before chromosome number snpVCFname: .dropGT.vcf.gz ###filename/extension of population vcf following chromosome number NormalBase: /opt/workdir/mergency/output/bam_normalMetrics ###path and filename of output form NormalMetrics step before chr number
cosmicVCF: /opt/workdir/DB/CosmicCodingMuts.vcf.gz ###path to cancer mutation count VCF refGenome: /opt/workdir/DB/hg19.fa ###path to reference genome that was used to align bams

User Inputs

outName: /opt/workdir/mergency/output/test ###path and filename base for output files outMat: /opt/workdir/mergency/output/test.mat ###path and filename for "mat" file (matlab data) export gvmPath: /lumosVar2/lumosVar2-master/bin/gvm ###path to folder containing gvm executable workingDirectory: /lumosVar2/lumosVar2-master/work/ ###poth to folder containing files in the "work" directory in the github repo NormalSample: 0 ###position in bamList of normal sample, 0 indicates tumor only priorF: [0.7] ###vector of expected tumor fractions with one value per bam, for example [0.1;0.7] for a pair of bams with low and high expected tumor content numCPU: 16 ### number of parallel processors how to solve this problem?thanks!

[jsonProgram]

hi,sunfengbao2017: How to fixed this problem?

thanks!

[rhalperin]

In your output directory, there should be a log file for each chromosome from the pileup step. Please share a the content of one of the log files.

On Monday, February 17, 2020, jsonProgram notifications@github.com wrote:

hi,sunfengbao2017: How to fixed this problem?

thanks!

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[jsonProgram]

@rhalperin Here is the ERROR i got in the log file ：

<<ERROR LOG [E::hts_open_format] Failed to open file 1.txt.gz [W::fai_get_val] Reference 1 not found in file, returning empty sequence gvm.c:1666: Failed to load reference genome from index. (err code -2)

gvm failed with status 1 on chr 1

ERROR LOG

And I got the bwa index in my reference path. ucsc.hg19.fasta ucsc.hg19.fasta.amb ucsc.hg19.fasta.ann ucsc.hg19.fasta.bwt ucsc.hg19.fasta.fai ucsc.hg19.fasta.pac ucsc.hg19.fasta.sa

[rhalperin]

It looks like the first error is trying to load the normal metrics file. Please make sure your "NormalBase" is correct in your yaml. For the reference genome as well as all of the other files paths in the yaml, please make sure you are using full paths rather than relative paths.

On Wed, Feb 19, 2020 at 1:08 AM jsonProgram notifications@github.com wrote:

@rhalperin https://github.com/rhalperin Here is the ERROR i got in the log file ：

<<ERROR LOG [E::hts_open_format] Failed to open file 1.txt.gz [W::fai_get_val] Reference 1 not found in file, returning empty sequence gvm.c:1666: Failed to load reference genome from index. (err code -2)

gvm failed with status 1 on chr 1

ERROR LOG

And I got the bwa index in my reference path. ucsc.hg19.fasta ucsc.hg19.fasta.amb ucsc.hg19.fasta.ann ucsc.hg19.fasta.bwt ucsc.hg19.fasta.fai ucsc.hg19.fasta.pac ucsc.hg19.fasta.sa

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[jsonProgram]

@rhalperin Thanks a lot !

Now I am running the test data which in http://tools.tgen.org/Files/lumosVar/

[a-jartseva]

@rhalperin Dear Rebecca, I ran into a similar issue when trying to test the functionality on just chromosome 21, as outlined here: http://tools.tgen.org/Files/lumosVar/Instructions.txt

The error message that I was getting was very similar to the one mentioned above:

Starting parallel pool (parpool) using the 'local' profile ... connected to 3 workers.
message =
gvm failed on 2
Output argument "T" (and maybe others) not assigned during call to "readBams".
Error in lumosVarMain (line 67)

In addition to the log file for chr21 in my output folder (HG02025_bamsurgeon_21.log.txt), I also noticed there was a log file called "HG02025bamsurgeon''.log.txt" created. When I checked the log for chr21, I did not see any errors; however, "HG02025bamsurgeon''.log.txt" contained the following:

[E::hts_open_format] Failed to open file /home/LumosVar/LumosVar_data/Example/Results/sureSelectV2_3bam_normalMetrics.txt.gz
[W::fai_get_val] Reference  not found in file, returning empty sequence
gvm.c:1666: Failed to load reference genome from index. (err code -2)

gvm failed with status 1 on chr ''

So essentially, it could not find the normal metrics file for chromosome ''. I believe that the field sexChr: '' in the config.yaml file is causing this issue - i.e. instead of ignoring the sex chromosomes, the software tries to process chromosome '', and of course it cannot do it. Leaving the corresponding field blank in the yaml file raised an error, as well. Therefore, something needs to be done to allow running lumosVarMain on single chromosomes as a test.

Thanks, Alex

[rhalperin]

Could you please give me more information on how you are running this so I can try to reproduce the issue? Did you download the latest commit or one of the releases? Are you running it with matlab or the binary using MCR?

[a-jartseva]

Hi, I cloned the github repo on 28/05/2020, so it must have included all the commits. I am running the binary using MCR 9.0.

I am sure that this issue is related to the sexChr: '' entry in the config.yaml file, since once I replaced '' with X, the issue disappeared. However, this means that running a test with just one autosome and no sex chromosomes is not working for me.

[rhalperin]

I apologize for the delay in addressing this issue, but it is now fixed in the latest release v1.04 Please note that the binary was compiled with a more recent version of Matlab and now needs to be run with MCR 9.4. The binary is too large to include in the repository is now attached to the release.

[a-jartseva]

Thank you, @rhalperin !