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tophat Preparing reads [FAILED]

Why is tophat giving this error message?

biostat1@biostat1-ubuntu:~/src/tools/test_data$ tophat2 -r 20 test_ref reads_1.fq reads_2.fq

[2014-05-24 17:02:09] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-05-24 17:02:09] Checking for Bowtie
          Bowtie version:     2.0.5.0
[2014-05-24 17:02:09] Checking for Samtools
        Samtools version:     0.1.17.0
[2014-05-24 17:02:09] Checking for Bowtie index files (genome)..
[2014-05-24 17:02:09] Checking for reference FASTA file
[2014-05-24 17:02:09] Generating SAM header for test_ref
[2014-05-24 17:02:09] Preparing reads
    [FAILED]
[Errno 8] Exec format error
tophat
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updated by Ram Ram • written by justinfanyi • justinfanyi

Look in the run log, it'll contain more information (including the last command run, which you could manually run to see the exact underlying error message).

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written by Devon Ryan Devon Ryan

Hi

Every seems to be alright on binary coz system (uname -a)

Linux biostat1-ubuntu 3.0.0-12-generic #20-Ubuntu SMP Fri Oct 7 14:50:42 UTC 2011 i686 athlon i386 GNU/Linux

here the run log:

home/biostat1/src/tools/tophat-2.0.11.Linux_x86_64/tophat -r 20 test_ref reads_1.fq reads_2.fq
#>prep_reads:
/home/biostat1/src/tools/tophat-2.0.11.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip --inner-dist-mean 20 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --aux-outfile=./tophat_out/prep_reads.info --index-outfile=./tophat_out/tmp/%side%_kept_reads.bam.index --sam-header=./tophat_out/tmp/test_ref_genome.bwt.samheader.sam --outfile=./tophat_out/tmp/%side%_kept_reads.bam reads_1.fq reads_2.fq

Looking forward to your help, thanks

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updated by Ram Ram • written by justinfanyi • justinfanyi

Do you still get the same error if you run that manually or do you get a different one? If it's the same, then perhaps you have a bad copy of the binary.

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written by Devon Ryan Devon Ryan

2 answers

Are you sure you've downloaded the right binary distributions for everything? "Exec format error" normally means you're trying to run something compiled for another architecture than you're actually running it on. I've inadvertently downloaded the MacOS X binaries for TopHat onto a Linux system in the past and had the same error.

And apparently not the only person to do so: [Errno 8] Exec Format Error Using Tophat 1.3.1

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updated by Ram Ram • written by User 59 User 59

Right binaries in place:

My system: 

Linux biostat1-ubuntu 3.0.0-12-generic #20-Ubuntu SMP Fri Oct 7 14:50:42 UTC 2011 i686 athlon i386 GNU/Linux

Tophat run log:

home/biostat1/src/tools/tophat-2.0.11.Linux_x86_64/tophat -r 20 test_ref reads_1.fq reads_2.fq
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updated by Ram Ram • written by justinfanyi • justinfanyi

i686 athlon i386 trying to run x86_64 binaries? I don't think that's going to work. i386/i686 = 32 bit architecture x86_64 = 64 bit architecture

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updated by Ram Ram • written by User 59 User 59

Sorry to revive an old thread, but I'm having this same problem.

I see that the cause above was running binaries for the wrong machine. I am running a 2015 MacBook Pro i7 with OSx Sierra. I have loaded the latest tophat through bioconda. I am running a tophat-env for python 2.7. When I run native on the machine, I get the 

        run_log = open(logging_dir + "run.log", "w", 0)
     ValueError: can't have unbuffered text I/O

which is caused due to lack of python3.5 support for tophat as noted on another thread.

Running with tophat-env activated, that error is solved and I get the same

[2016-12-07 17:11:23] Preparing reads
[FAILED]
[Errno 8] Exec format error

experienced by others here.

I have completely re-installed anaconda package and tophat and tophat-env, with same results.

I trust bioconda to install the appropriate binaries, but how can I verify this?

Other suggestions?

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written by mike • mike

I had the same problem with you . and I do not know why, Did you fix it?

Traceback (most recent call last):

  File "/home/z800/miniconda3/bin/tophat", line 4107, in <module>
    sys.exit(main())

  File "/home/z800/miniconda3/bin/tophat", line 3899, in main
    run_log = open(logging_dir + "run.log", "w", 0)

ValueError: can't have unbuffered text I/O
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updated by Ram Ram • written by Ada • Ada

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