chr20.gp.vcf.gz: No such file or directory

[dipingxian431]

Hi, I am running Germline, after successfully running preProcess. I met a few problems. First, when I ran germline, the output showed that I didn't have Java. So, I installed Java using conda install bioconda::java-jdk . After that, I rerun it. the output showed that no bam.bai file. So, I used the samtools index to add the bai file. Then re-run Germine with the following command.

path="/home/mingchao/Linux_file/Monopogen/Monopogen"  # where Monopogen is downloaded
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${path}/apps
python  ${path}/src/Monopogen.py  germline  \
    -a   ${path}/apps -r  /data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/region.lst \
    -p  /data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/  \
    -g  /data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/chr20_2Mb.hg38.fa   -s all  -o /data/Mingchao/dowload_data/Monopogen/Monopogen_testout

The job still cannot run correctly. The output file only has chr20.gl.vcf.gz and the size is 0. But at the end of the report shows "Monopogen.py Success! See instructions above."

The Monopogen_testout files:

drwxrwxr-x+ 2 mingchao mingchao 4096 Apr  7 16:48 ./
drwxrwxr-x+ 5 mingchao mingchao 4096 Apr  7 13:17 ../
-rw-rw-r--+ 1 mingchao mingchao    0 Apr  7 16:48 chr20.gl.vcf.gz
-rw-rw-r--+ 1 mingchao mingchao  692 Apr  7 16:48 chr20.gp.log
-rw-rw-r--+ 1 mingchao mingchao  699 Apr  7 16:48 chr20.phased.log

The output report:

[2024-04-07 16:48:08,516] INFO     Monopogen.py Performing germline variant calling...
[2024-04-07 16:48:08,517] INFO     germline.py Parameters in effect:
[2024-04-07 16:48:08,517] INFO     germline.py --subcommand = [germline]
[2024-04-07 16:48:08,517] INFO     germline.py --region = [/data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/region.lst]
[2024-04-07 16:48:08,517] INFO     germline.py --step = [all]
[2024-04-07 16:48:08,517] INFO     germline.py --out = [/data/Mingchao/dowload_data/Monopogen/Monopogen_testout]
[2024-04-07 16:48:08,517] INFO     germline.py --reference = [/data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/chr20_2Mb.hg38.fa]
[2024-04-07 16:48:08,517] INFO     germline.py --imputation_panel = [/data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/]
[2024-04-07 16:48:08,517] INFO     germline.py --max_softClipped = [1]
[2024-04-07 16:48:08,517] INFO     germline.py --app_path = [/home/mingchao/Linux_file/Monopogen/Monopogen/apps]
[2024-04-07 16:48:08,517] INFO     germline.py --nthreads = [1]
[2024-04-07 16:48:08,517] INFO     germline.py --norun = [FALSE]
[2024-04-07 16:48:08,517] INFO     Monopogen.py Checking existence of essenstial resource files...
[2024-04-07 16:48:08,517] INFO     Monopogen.py Checking dependencies...
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/samtools: Permission denied
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bcftools: Permission denied
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bcftools: Permission denied
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh: line 1: /home/mingchao/Linux_file/Monopogen/Monopogen/apps/bgzip: Permission denied
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: 04:48 PM EDT on 07 Apr 2024

Command line: java -Xmx18204m -jar beagle.jar
  gl=/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.gl.vcf.gz
  ref=/data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz
  chrom=chr20
  out=/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.gp
  impute=false
  modelscale=2
  nthreads=24
  gprobs=true
  niterations=0

No genetic map is specified: using 1 cM = 1 Mb
java.io.EOFException
        at java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268)
        at java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:258)
        at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:164)
        at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
        at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
        at blbutil.InputIt.fromGzipFile(InputIt.java:214)
        at main.Main.allData(Main.java:302)
        at main.Main.main(Main.java:111)
java.io.EOFException
Error reading /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.gl.vcf.gz
terminating program.
gzip: /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/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: 04:48 PM EDT on 07 Apr 2024

Command line: java -Xmx18204m -jar beagle.jar
  gt=/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.germline.vcf
  ref=/data/Mingchao/dowload_data/Monopogen/Monopogen_testfile/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz
  chrom=chr20
  out=/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/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: /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.germline.vcf
/data/Mingchao/dowload_data/Monopogen/Monopogen_testout/germline/chr20.gp.vcf.gz: No such file or directory
        at vcf.VcfHeader.checkHeaderLine(VcfHeader.java:135)
        at vcf.VcfHeader.<init>(VcfHeader.java:119)
        at vcf.VcfIt.<init>(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)
bash /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh
[2024-04-07 16:48:08,799] INFO     Monopogen.py Success! See instructions above.
['bash /data/Mingchao/dowload_data/Monopogen/Monopogen_testout/Script/runGermline_chr20.sh']

Any guidance to resolve this would be helpful.

Thank you so much!