1. Charlie Xia Avatar Charlie Xia
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OSError: [Errno 8] Exec format error

Issue #1 resolved
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Hi Charlie,

I'm trying to use SVEngine. However, I got two kinds of error messages when running test_mf.sh. Could you give me some ideas on why those happen and how I can solve those issues. Thank you very much!

  1. I got this for all testings, except "### testing output fasta" in var2fq... fakefq: processing 2 out of 190 regions Traceback (most recent call last): File "/share/ScratchGeneral/tingon/miniconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main "main", fname, loader, pkg_name) File "/share/ScratchGeneral/tingon/miniconda2/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 1346, in <module> run() File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 1343, in run main(args) File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 335, in main ffq = var2fq(Bunch(dic)) File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 522, in var2fq bedfqs.append(fakefq(hapit)) File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 623, in fakefq wgs0 = fqwgs(parlist,nligation,reffile,nploidy,[seq0],lib,freq0,mergemax,outfastq) File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 699, in fqwgs runcmd(wgs_cmd) #fastq file File "/share/ScratchGeneral/tingon/svengine/svengine/mf/mutforge.py", line 87, in runcmd run=subprocess.Popen(cmd.split(),env=os.environ,cwd=os.getcwd(),stderr=subprocess.PIPE,stdout=subprocess.PIPE) File "/share/ScratchGeneral/tingon/miniconda2/lib/python2.7/subprocess.py", line 390, in init errread, errwrite) File "/share/ScratchGeneral/tingon/miniconda2/lib/python2.7/subprocess.py", line 1025, in _execute_child raise child_exception OSError: [Errno 8] Exec format error

  2. testing using a VAR file (.var) input

    tmpdir= /home/tingon/svetmp_vEvz preparing simulation regions... done entering runmode 3 in file2var ... file2var done in var2bed ... done var2bed in var2fq... ERROR: feature 2 3708000 3708001 VAR_1 FINS_1 0.5 0 example.fas,fins1:1-1200,1,f 2 12000 13001 VAR_5 ITRA_1 0.5 1000 None 2 3722000 3722001 VAR_7 ITRA_1 0.5 0 example.fna,2:12001-13000,1,r 1 12000 13001 VAR_9 ITRA_2 0.5 1000 None 2 3736000 3736001 VAR_11 ITRA_2 0.5 0 example.fna,1:12001-13000,1,r 1 26000 28001 VAR_15 DEL_2 1.0 2000 None 2 26000 28001 VAR_17 DEL_3 1.0 2000 None 2 40000 41001 VAR_21 TRA_1 1.0 1000 None 1 40000 40001 VAR_23 TRA_1 0.5 0 example.fna,2:40001-41000,1,f 2 54000 54001 VAR_27 TRA_2 0.5 0 example.fna,2:138001-139000,1,f 2 3750000 3751001 VAR_29 INV_1 0.5 1000 example.fna,2:3750001-3751000,1,r 1 54000 55001 VAR_31 INV_2 0.5 1000 example.fna,1:54001-55000,1,r 1 1636000 1637001 VAR_33 IDUP_1 0.5 1000 example.fna,1:1636001-1637000,2,r 2 68000 69001 VAR_35 IDUP_2 0.5 1000 example.fna,2:68001-69000,2,r 1 68000 68001 VAR_37 DINS_1 0.5 0 example.fna,1:124001-125000,1,f 2 3764000 3764001 VAR_39 DINS_2 0.5 0 example.fna,2:152001-153000,1,f 1 82000 82001 VAR_41 IDINS_1 0.5 0 example.fna,2:82001-83000,1,r

not overlapping any simulation region, correct your input

Comments (9)

  1. Charlie Xia repo owner

    Hi. I cannot replicate this on my ubuntu and mac with python 2.7. Can you let me know your system and python.

    Note, if it is a platform or python distro specific issue, You can always use the Dockerfile provided to ran svengine in a docker container.

  3. Tingting Gong

    Hi Charlie,

    Thank you for the quick reply. I'm working on the HPC cluster. Python used: virtual environment from python-2.7.9 installed and I also tried python-2.7.14 by miniconda2 I still got the error messages.

    Sorry for the stupid question that what is Dockerfile and how can I use that for svengine? Do you mean the aws EC2 instance?

    Thank you very much, Tingting

  4. Charlie Xia repo owner

    No, not any question is stupid. Briefly, you can understand Docker as a cross-platform virtual machine. It is available for Linux, Mac and MS Windows. https://www.docker.com

    After you've install it on your local system and learn the basics. You've just need to download the Dockerfile from the SVEngine repo and put it in a directory say sve_docker, and then build a container from inside the directory: docker build

    It will give you a container id and you can then access the SVEngine by running the container VM by: docker exec -it $your_container_id /bin/bash

  5. Tingting Gong

    Thank you very much for the help. I used another HPC platform and python 2.7.11. But I got the same error message: tmpdir= /home/913/tg2182/svetmp_LlRk preparing simulation regions... done entering runmode 1 output varcnt 48 in var2file... done var2file in var2bed ... done var2bed in var2fq... fakefq: processing 2 out of 192 regions Traceback (most recent call last): File "/apps/python/2.7.11/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/apps/python/2.7.11/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 1346, in <module> run() File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 1343, in run main(args) File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 335, in main ffq = var2fq(Bunch(dic)) File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 522, in var2fq bedfqs.append(fakefq(hapit)) File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 632, in fakefq wgs1 = fqwgs(parlist,nligation,reffile,nploidy,[seq1],lib,freq1,mergemax,outfastq) File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 699, in fqwgs runcmd(wgs_cmd) #fastq file File "/short/qa2/tg2182/svengine/svengine/mf/mutforge.py", line 87, in runcmd run=subprocess.Popen(cmd.split(),env=os.environ,cwd=os.getcwd(),stderr=subprocess.PIPE,stdout=subprocess.PIPE) File "/apps/python/2.7.11/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/apps/python/2.7.11/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 8] Exec format error

    I have tested with fasta output sucessfully as following, but not fastq and bam. PYTHONPATH=$SVENGINEPATH python -m mf.mutforge -x fasta -n 1 -b 100000 -f 10000 -e 100000 -m test_mf.meta example.fna simple.par example.fna Could you give me some ideas about this? How -x bam or -x fastq work differently with -x fasta? What I may got wrong or miss?

    Dockerfile: I tried to ran svengine in docker container on my mac. But got: Cloning into 'svengine'... error: RPC failed; curl 56 GnuTLS recv error (-9): A TLS packet with unexpected length was received. fatal: The remote end hung up unexpectedly fatal: early EOF fatal: index-pack failed I will see how to solve that to make svengine work. Please let me know if you know what is wrong here.

    Thank you.

  7. Charlie Xia repo owner

    Think I fixed the "Exec format error" issue. The reason is I only shipped a binary xwgsim with the package. I also fixed the "RPC error" thing. Thanks for catching the bug. Now you are free to use it either way.

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