jinzhuangdou
commented
6 months ago Hi the error shows "/rsrch5/home/tdccct/ppshah/shared/pipelines/Monopogen/apps/bcftools: error while loading shared libraries: ". Could you try to see whether it works (as mentioned in FAQs)?
bcftools: error while loading shared libraries: libbz2.so.1.0: not able to open shared object file: No such file or directly Adding the apps folder of Monopogen in your library environment export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/xx/apps
parth2608
Hi, I am trying to run Germline on the example provided in the repository. After successfully running preProcess, I run the following command:
python src/Monopogen.py germline -a apps/ -t 1 -r test/region.lst -p example/ -g example/chr20_2Mb.hg38.fa -s all -o out
But I get errors and the following is the output:
[2024-01-09 11:42:35,227] INFO Monopogen.py Performing germline variant calling... [2024-01-09 11:42:35,227] INFO germline.py Parameters in effect: [2024-01-09 11:42:35,227] INFO germline.py --subcommand = [germline] [2024-01-09 11:42:35,227] INFO germline.py --region = [test/region.lst] [2024-01-09 11:42:35,227] INFO germline.py --step = [all] [2024-01-09 11:42:35,227] INFO germline.py --out = [out] [2024-01-09 11:42:35,227] INFO germline.py --reference = [example/chr20_2Mb.hg38.fa] [2024-01-09 11:42:35,228] INFO germline.py --imputation_panel = [example/] [2024-01-09 11:42:35,228] INFO germline.py --max_softClipped = [1] [2024-01-09 11:42:35,228] INFO germline.py --app_path = [apps/] [2024-01-09 11:42:35,228] INFO germline.py --nthreads = [1] [2024-01-09 11:42:35,228] INFO germline.py --norun = [FALSE] [2024-01-09 11:42:35,228] INFO Monopogen.py Checking existence of essenstial resource files... [2024-01-09 11:42:35,236] INFO Monopogen.py Checking dependencies... ['bash out/Script/runGermline_chr20.sh'] /rsrch5/home/tdccct/ppshah/shared/pipelines/Monopogen/apps/bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory /rsrch5/home/tdccct/ppshah/shared/pipelines/Monopogen/apps/bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory [mpileup] 2 samples in 2 input files (mpileup) Max depth is above 1M. Potential memory hog! beagle.27Jul16.86a.jar (version 4.1) Copyright (C) 2014-2015 Brian L. Browning Enter "java -jar beagle.27Jul16.86a.jar" for a summary of command line arguments. Start time: 11:44 AM CST on 09 Jan 2024
Command line: java -Xmx20480m -jar beagle.jar gl=out/germline/chr20.gl.vcf.gz ref=example/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz chrom=chr20 out=out/germline/chr20.gp impute=false modelscale=2 nthreads=24 gprobs=true niterations=0
No genetic map is specified: using 1 cM = 1 Mb Exception in thread "main" java.lang.IllegalArgumentException: Missing line (#CHROM ...) after meta-information lines File source: out/germline/chr20.gl.vcf.gz null at vcf.VcfHeader.checkHeaderLine(VcfHeader.java:135) at vcf.VcfHeader.(VcfHeader.java:119)
at vcf.VcfIt.(VcfIt.java:190)
at vcf.VcfIt.create(VcfIt.java:175)
at vcf.VcfIt.create(VcfIt.java:150)
at main.Main.allData(Main.java:303)
at main.Main.main(Main.java:111)
gzip: out/germline/chr20.gp.vcf.gz: No such file or directory
out/germline/chr20.gp.vcf.gz: No such file or directory
beagle.27Jul16.86a.jar (version 4.1)
Copyright (C) 2014-2015 Brian L. Browning
Enter "java -jar beagle.27Jul16.86a.jar" for a summary of command line arguments.
Start time: 11:44 AM CST on 09 Jan 2024
Command line: java -Xmx20480m -jar beagle.jar gt=out/germline/chr20.germline.vcf ref=example/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz chrom=chr20 out=out/germline/chr20.phased impute=false modelscale=2 nthreads=24 gprobs=true niterations=0
No genetic map is specified: using 1 cM = 1 Mb Exception in thread "main" java.lang.IllegalArgumentException: Missing line (#CHROM ...) after meta-information lines File source: out/germline/chr20.germline.vcf null at vcf.VcfHeader.checkHeaderLine(VcfHeader.java:135) at vcf.VcfHeader.(VcfHeader.java:119)
at vcf.VcfIt.(VcfIt.java:190)
at vcf.VcfIt.create(VcfIt.java:175)
at vcf.VcfIt.create(VcfIt.java:150)
at main.Main.allData(Main.java:297)
at main.Main.main(Main.java:111)
[2024-01-09 11:44:08,145] INFO Monopogen.py Success! See instructions above.
Any guidance to resolve this would be helpful. I am working on HPC system.
Thank you!