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chr20.gp.vcf.gz: No such file or directory #50

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dipingxian431 opened this issue Apr 7, 2024 · 5 comments
Open

chr20.gp.vcf.gz: No such file or directory #50

dipingxian431 opened this issue Apr 7, 2024 · 5 comments

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@dipingxian431
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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!
@jinzhuangdou
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It shows errors as following:
/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
Could you set execute permission on /home/mingchao/Linux_file/Monopogen/Monopogen/apps/*? For example chmod g+x

@dipingxian431
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Thank you so much for the reply!

I tried to execute the permission by using chmod g+x /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/*
before:

(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ll
total 41076
drwxrwxr-x 2 mingchao mingchao     4096 Apr  7 22:23 ./
drwxrwxr-x 9 mingchao mingchao     4096 Apr  7 21:59 ../
-rw-rw-r-- 1 mingchao mingchao  1939857 Apr  7 21:59 bcftools
-rw-rw-r-- 1 mingchao mingchao   300906 Apr  7 21:59 beagle.08Feb22.fa4.jar
-rw-rw-r-- 1 mingchao mingchao   330554 Apr  7 21:59 beagle.27Jul16.86a.jar
-rw-rw-r-- 1 mingchao mingchao   631018 Apr  7 21:59 bgzip
-rw-rw-r-- 1 mingchao mingchao   100800 Apr  7 21:59 gzip
-rw-rw-r-- 1 mingchao mingchao    12784 Apr  7 21:59 java
-rw-rw-r-- 1 mingchao mingchao    68192 Apr  7 21:59 libbz2.so.1.0
-rw-rw-r-- 1 mingchao mingchao  3152968 Apr  7 21:59 libcrypto.so.1.0.0
-rw-rw-r-- 1 mingchao mingchao    64528 Apr  7 21:59 libdeflate.so
-rw-rw-r-- 1 mingchao mingchao 17389398 Apr  7 21:59 picard.jar
-rw-rw-r-- 1 mingchao mingchao  2911966 Apr  7 21:59 samtools
-rw-rw-r-- 1 mingchao mingchao   683232 Apr  7 21:59 tabix
-rw-rw-r-- 1 mingchao mingchao 14444639 Apr  7 21:59 vcftools

After:

(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ll
total 41076
drwxrwxr-x 2 mingchao mingchao     4096 Apr  7 22:23 ./
drwxrwxr-x 9 mingchao mingchao     4096 Apr  7 21:59 ../
-rw-rwxr-- 1 mingchao mingchao  1939857 Apr  7 21:59 bcftools*
-rw-rwxr-- 1 mingchao mingchao   300906 Apr  7 21:59 beagle.08Feb22.fa4.jar*
-rw-rwxr-- 1 mingchao mingchao   330554 Apr  7 21:59 beagle.27Jul16.86a.jar*
-rw-rwxr-- 1 mingchao mingchao   631018 Apr  7 21:59 bgzip*
-rw-rwxr-- 1 mingchao mingchao   100800 Apr  7 21:59 gzip*
-rw-rwxr-- 1 mingchao mingchao    12784 Apr  7 21:59 java*
-rw-rwxr-- 1 mingchao mingchao    68192 Apr  7 21:59 libbz2.so.1.0*
-rw-rwxr-- 1 mingchao mingchao  3152968 Apr  7 21:59 libcrypto.so.1.0.0*
-rw-rwxr-- 1 mingchao mingchao    64528 Apr  7 21:59 libdeflate.so*
-rw-rwxr-- 1 mingchao mingchao 17389398 Apr  7 21:59 picard.jar*
-rw-rwxr-- 1 mingchao mingchao  2911966 Apr  7 21:59 samtools*
-rw-rwxr-- 1 mingchao mingchao   683232 Apr  7 21:59 tabix*
-rw-rwxr-- 1 mingchao mingchao 14444639 Apr  7 21:59 vcftools*

I also test them by using /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/samtools the output still permission denied:-bash: /home/mingchao/Linux_file/Monopogen2/Monopogen/apps/samtools: Permission denied.
Same as another one:
(Variants) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./gzip -h
-bash: ./gzip: Permission denied

What should I do next?

Thank you so much!

@jinzhuangdou
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jinzhuangdou commented Apr 8, 2024 •
edited
Loading

Could you try chmod u+x ./*. Using g+x only allows the group not the owner with the executing permission.

@dipingxian431
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Thank you for the reply!

I tried hmod u+x ./*. But new questions come.

(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./bcftools 
./bcftools: error while loading shared libraries: libdeflate.so: cannot open shared object file: No such file or directory
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./samtools
./samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory

And I can not use sudo apt-get install libncurses5 to install.
Do you have some other suggestions?
Thank you!

@dipingxian431
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I also test other apps. It looks like all of them cannot be right run now.

(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./beagle.08Feb22.fa4.jar
-bash: ./beagle.08Feb22.fa4.jar: cannot execute binary file: Exec format error
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./bgzip 
./bgzip: error while loading shared libraries: libdeflate.so: cannot open shared object file: No such file or directory
(base) mingchao@JS-Lambda-Vector:~/Linux_file/Monopogen2/Monopogen/apps$ ./libbz2.so.1.0 
Segmentation fault (core dumped)

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@jinzhuangdou @dipingxian431